Class: AssayOutputMeasurement

The measurement results produced by an assay. The specified output of a planned process. Each domain-specific assay class has a corresponding AssayOutputMeasurement subclass containing the named measurement slots for that assay type. This class represents the "output" in the Input/Process/Output model: what was measured and what values were obtained.

One AssayOutputMeasurement record represents the results for ONE experimental condition or group. When a study reports a control group and one or more treated groups (or a dose-response series), each group gets its own output record, marked with experimental_group and linked to the specific exposure condition via measured_under.

When a paper reports a result only as a chart or image (a bar graph, a stained section) and no exact number appears in the text, still create the output record: set data_in_figure_only, leave the numeric measurement slots empty, and attach an evidence item whose figure_reference names the figure, so the endpoint and its location are captured even though the value is not.

NOTE: this is an abstract class and should not be instantiated directly

URI: soma:AssayOutputMeasurement

 classDiagram
    class AssayOutputMeasurement
    click AssayOutputMeasurement href "../AssayOutputMeasurement/"
      NamedThing <|-- AssayOutputMeasurement
        click NamedThing href "../NamedThing/"


      AssayOutputMeasurement <|-- CiliaryFunctionOutput
        click CiliaryFunctionOutput href "../CiliaryFunctionOutput/"
      AssayOutputMeasurement <|-- ASLOutput
        click ASLOutput href "../ASLOutput/"
      AssayOutputMeasurement <|-- MucociliaryClearanceOutput
        click MucociliaryClearanceOutput href "../MucociliaryClearanceOutput/"
      AssayOutputMeasurement <|-- OxidativeStressOutput
        click OxidativeStressOutput href "../OxidativeStressOutput/"
      AssayOutputMeasurement <|-- CFTRFunctionOutput
        click CFTRFunctionOutput href "../CFTRFunctionOutput/"
      AssayOutputMeasurement <|-- EGFRSignalingOutput
        click EGFRSignalingOutput href "../EGFRSignalingOutput/"
      AssayOutputMeasurement <|-- GobletCellOutput
        click GobletCellOutput href "../GobletCellOutput/"
      AssayOutputMeasurement <|-- BALFSputumOutput
        click BALFSputumOutput href "../BALFSputumOutput/"
      AssayOutputMeasurement <|-- LungFunctionOutput
        click LungFunctionOutput href "../LungFunctionOutput/"
      AssayOutputMeasurement <|-- FoxJExpressionOutput
        click FoxJExpressionOutput href "../FoxJExpressionOutput/"
      AssayOutputMeasurement <|-- GeneExpressionOutput
        click GeneExpressionOutput href "../GeneExpressionOutput/"


      AssayOutputMeasurement : data_in_figure_only

      AssayOutputMeasurement : description

      AssayOutputMeasurement : evidence





        AssayOutputMeasurement --> "* _recommended_" EvidenceItem : evidence
        click EvidenceItem href "../EvidenceItem/"



      AssayOutputMeasurement : experimental_group





        AssayOutputMeasurement --> "0..1" ExperimentalGroupEnum : experimental_group
        click ExperimentalGroupEnum href "../ExperimentalGroupEnum/"



      AssayOutputMeasurement : id

      AssayOutputMeasurement : measured_under





        AssayOutputMeasurement --> "0..1" ExposureCondition : measured_under
        click ExposureCondition href "../ExposureCondition/"



      AssayOutputMeasurement : name

Inheritance

NamedThing
- AssayOutputMeasurement

Slots

Name	Cardinality and Range	Description	Inheritance
evidence	* recommended EvidenceItem	Evidence items backing this object's claims	direct
experimental_group	0..1 ExperimentalGroupEnum	The role of this output record's group in the experimental design: control, v...	direct
measured_under	0..1 ExposureCondition	Reference (by id) to the specific ExposureCondition this output record was me...	direct
data_in_figure_only	0..1 Boolean	True when the quantitative values for this output record are reported only in...	direct
id	1 Uriorcurie	A unique identifier for the entity	NamedThing
name	0..1 String	A human-readable name for the entity	NamedThing
description	0..1 String	A detailed description of the entity	NamedThing

Usages

used by	used in	type	used
Assay	has_specified_output	range	AssayOutputMeasurement
ResponseComparison	control_output	range	AssayOutputMeasurement
ResponseComparison	treated_output	range	AssayOutputMeasurement

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/EHS-Data-Standards/soma

Mappings

Mapping Type	Mapped Value
self	soma:AssayOutputMeasurement
native	soma:AssayOutputMeasurement
exact	IAO:0000109

LinkML Source

Direct

name: AssayOutputMeasurement
description: 'The measurement results produced by an assay. The specified output of
  a planned process. Each domain-specific assay class has a corresponding AssayOutputMeasurement
  subclass containing the named measurement slots for that assay type. This class
  represents the "output" in the Input/Process/Output model: what was measured and
  what values were obtained.

  One AssayOutputMeasurement record represents the results for ONE experimental condition
  or group. When a study reports a control group and one or more treated groups (or
  a dose-response series), each group gets its own output record, marked with experimental_group
  and linked to the specific exposure condition via measured_under.

  When a paper reports a result only as a chart or image (a bar graph, a stained section)
  and no exact number appears in the text, still create the output record: set data_in_figure_only,
  leave the numeric measurement slots empty, and attach an evidence item whose figure_reference
  names the figure, so the endpoint and its location are captured even though the
  value is not.'
from_schema: https://w3id.org/EHS-Data-Standards/soma
exact_mappings:
- IAO:0000109
is_a: NamedThing
abstract: true
slots:
- evidence
- experimental_group
- measured_under
- data_in_figure_only

Induced

name: AssayOutputMeasurement
description: 'The measurement results produced by an assay. The specified output of
  a planned process. Each domain-specific assay class has a corresponding AssayOutputMeasurement
  subclass containing the named measurement slots for that assay type. This class
  represents the "output" in the Input/Process/Output model: what was measured and
  what values were obtained.

  One AssayOutputMeasurement record represents the results for ONE experimental condition
  or group. When a study reports a control group and one or more treated groups (or
  a dose-response series), each group gets its own output record, marked with experimental_group
  and linked to the specific exposure condition via measured_under.

  When a paper reports a result only as a chart or image (a bar graph, a stained section)
  and no exact number appears in the text, still create the output record: set data_in_figure_only,
  leave the numeric measurement slots empty, and attach an evidence item whose figure_reference
  names the figure, so the endpoint and its location are captured even though the
  value is not.'
from_schema: https://w3id.org/EHS-Data-Standards/soma
exact_mappings:
- IAO:0000109
is_a: NamedThing
abstract: true
attributes:
  evidence:
    name: evidence
    description: Evidence items backing this object's claims. Each one carries an
      exact quote from a cited publication.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: evidence
    owner: AssayOutputMeasurement
    domain_of:
    - KeyEvent
    - KeyEventRelationship
    - Assay
    - AssayOutputMeasurement
    range: EvidenceItem
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  experimental_group:
    name: experimental_group
    description: 'The role of this output record''s group in the experimental design:
      control, vehicle control, baseline, treated, recovery, or sham. Lets extraction
      distinguish the control/baseline response from the treated response so a change
      relative to control can be assembled downstream.'
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: experimental_group
    owner: AssayOutputMeasurement
    domain_of:
    - AssayOutputMeasurement
    range: ExperimentalGroupEnum
  measured_under:
    name: measured_under
    description: Reference (by id) to the specific ExposureCondition this output record
      was measured under. Links each set of response values to the concentration/treatment
      it corresponds to, so a dose-response series keeps each response paired with
      its exposure level. The referenced condition should be listed in the assay's
      has_exposure_condition.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: measured_under
    owner: AssayOutputMeasurement
    domain_of:
    - AssayOutputMeasurement
    range: ExposureCondition
    inlined: false
  data_in_figure_only:
    name: data_in_figure_only
    description: True when the quantitative values for this output record are reported
      only in a figure or chart and could not be read from the text. The record then
      documents that the endpoint was measured and where its data lives (via an evidence
      item's figure_reference and article_section), without numeric values. This keeps
      figure-only results visible to reviewers in the workbook instead of silently
      dropping them.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: data_in_figure_only
    owner: AssayOutputMeasurement
    domain_of:
    - AssayOutputMeasurement
    range: boolean
  id:
    name: id
    description: A unique identifier for the entity.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    identifier: true
    alias: id
    owner: AssayOutputMeasurement
    domain_of:
    - NamedThing
    - Unit
    - NamedEntity
    range: uriorcurie
    required: true
  name:
    name: name
    description: A human-readable name for the entity.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    slot_uri: schema:name
    alias: name
    owner: AssayOutputMeasurement
    domain_of:
    - NamedThing
    - Unit
    - NamedEntity
    range: string
  description:
    name: description
    description: A detailed description of the entity.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    slot_uri: schema:description
    alias: description
    owner: AssayOutputMeasurement
    domain_of:
    - NamedThing
    range: string