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Class: OxidativeStressMeasurement

Measurement of oxidative stress markers

URI: outcomes_model:OxidativeStressMeasurement

classDiagram class OxidativeStressMeasurement click OxidativeStressMeasurement href "../OxidativeStressMeasurement/" Measurement <|-- OxidativeStressMeasurement click Measurement href "../Measurement/" OxidativeStressMeasurement : antioxidant_capacity OxidativeStressMeasurement --> "0..1" QuantityValue : antioxidant_capacity click QuantityValue href "../QuantityValue/" OxidativeStressMeasurement : antioxidant_enzyme_activities OxidativeStressMeasurement : description OxidativeStressMeasurement : detection_method_details OxidativeStressMeasurement --> "*" DetectionMethod : detection_method_details click DetectionMethod href "../DetectionMethod/" OxidativeStressMeasurement : dna_damage_markers OxidativeStressMeasurement --> "0..1" QuantityValue : dna_damage_markers click QuantityValue href "../QuantityValue/" OxidativeStressMeasurement : id OxidativeStressMeasurement : input_sample OxidativeStressMeasurement --> "0..1" InputSample : input_sample click InputSample href "../InputSample/" OxidativeStressMeasurement : lipid_peroxidation OxidativeStressMeasurement --> "0..1" QuantityValue : lipid_peroxidation click QuantityValue href "../QuantityValue/" OxidativeStressMeasurement : media_composition OxidativeStressMeasurement : method_assay OxidativeStressMeasurement --> "0..1" Assay : method_assay click Assay href "../Assay/" OxidativeStressMeasurement : protein_oxidation_markers OxidativeStressMeasurement : protocol_notes OxidativeStressMeasurement : ros_level OxidativeStressMeasurement --> "0..1" QuantityValue : ros_level click QuantityValue href "../QuantityValue/" OxidativeStressMeasurement : ros_probe OxidativeStressMeasurement --> "0..1" ROSProbe : ros_probe click ROSProbe href "../ROSProbe/"

Inheritance

Slots

Name Cardinality and Range Description Inheritance
ros_level 0..1
QuantityValue		 Reactive oxygen species level direct
lipid_peroxidation 0..1
QuantityValue		 Lipid peroxidation markers (MDA, 8-isoprostane, etc direct
antioxidant_capacity 0..1
QuantityValue		 Antioxidant capacity (GSH/GSSG ratio, enzyme activity) direct
ros_probe 0..1
ROSProbe		 ROS probe details direct
detection_method_details *
DetectionMethod		 Detection method details direct
protein_oxidation_markers *
String		 Protein oxidation markers (carbonyls, nitrotyrosine) direct
dna_damage_markers 0..1
QuantityValue		 DNA damage markers (8-OHdG) direct
antioxidant_enzyme_activities 0..1
String		 Antioxidant enzyme activities (SOD, catalase, GPx) direct
media_composition 0..1
String		 Culture media composition details for in vitro oxidative stress measures direct
input_sample 0..1
InputSample		 Description of input samples and manipulations Measurement
method_assay 0..1
Assay		 The method or assay used Measurement
protocol_notes 0..1
String		 Protocol or SOP notes Measurement
id 1
Uriorcurie		 A unique identifier NamedEntity
description 0..1
String		 A detailed description NamedEntity

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/EHS-Data-Standards/outcomes-model

Mappings

Mapping Type Mapped Value
self outcomes_model:OxidativeStressMeasurement
native outcomes_model:OxidativeStressMeasurement

LinkML Source

Direct

name: OxidativeStressMeasurement
description: Measurement of oxidative stress markers
from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
is_a: Measurement
slots:
- ros_level
- lipid_peroxidation
- antioxidant_capacity
- ros_probe
- detection_method_details
- protein_oxidation_markers
- dna_damage_markers
- antioxidant_enzyme_activities
- media_composition

Induced

name: OxidativeStressMeasurement
description: Measurement of oxidative stress markers
from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
is_a: Measurement
attributes:
  ros_level:
    name: ros_level
    description: Reactive oxygen species level
    from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
    related_mappings:
    - CHEBI:26523
    broad_mappings:
    - PATO:0000070
    rank: 1000
    alias: ros_level
    owner: OxidativeStressMeasurement
    domain_of:
    - OxidativeStressMeasurement
    range: QuantityValue
    inlined: true
  lipid_peroxidation:
    name: lipid_peroxidation
    description: Lipid peroxidation markers (MDA, 8-isoprostane, etc.)
    from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
    related_mappings:
    - GO:0016491
    rank: 1000
    alias: lipid_peroxidation
    owner: OxidativeStressMeasurement
    domain_of:
    - OxidativeStressMeasurement
    range: QuantityValue
    inlined: true
  antioxidant_capacity:
    name: antioxidant_capacity
    description: Antioxidant capacity (GSH/GSSG ratio, enzyme activity)
    from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
    rank: 1000
    alias: antioxidant_capacity
    owner: OxidativeStressMeasurement
    domain_of:
    - OxidativeStressMeasurement
    range: QuantityValue
    inlined: true
  ros_probe:
    name: ros_probe
    description: ROS probe details
    from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
    rank: 1000
    alias: ros_probe
    owner: OxidativeStressMeasurement
    domain_of:
    - OxidativeStressMeasurement
    range: ROSProbe
    inlined: true
  detection_method_details:
    name: detection_method_details
    description: Detection method details
    from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
    broad_mappings:
    - OBI:0000070
    rank: 1000
    alias: detection_method_details
    owner: OxidativeStressMeasurement
    domain_of:
    - OxidativeStressMeasurement
    range: DetectionMethod
    multivalued: true
    inlined: true
  protein_oxidation_markers:
    name: protein_oxidation_markers
    description: Protein oxidation markers (carbonyls, nitrotyrosine)
    from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
    rank: 1000
    alias: protein_oxidation_markers
    owner: OxidativeStressMeasurement
    domain_of:
    - OxidativeStressMeasurement
    range: string
    multivalued: true
  dna_damage_markers:
    name: dna_damage_markers
    description: DNA damage markers (8-OHdG)
    from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
    rank: 1000
    alias: dna_damage_markers
    owner: OxidativeStressMeasurement
    domain_of:
    - OxidativeStressMeasurement
    range: QuantityValue
    inlined: true
  antioxidant_enzyme_activities:
    name: antioxidant_enzyme_activities
    description: Antioxidant enzyme activities (SOD, catalase, GPx)
    from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
    rank: 1000
    alias: antioxidant_enzyme_activities
    owner: OxidativeStressMeasurement
    domain_of:
    - OxidativeStressMeasurement
    range: string
  media_composition:
    name: media_composition
    description: Culture media composition details for in vitro oxidative stress measures
    comments:
    - Critical for oxidative stress measurements as media components can affect ROS
    from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
    rank: 1000
    alias: media_composition
    owner: OxidativeStressMeasurement
    domain_of:
    - OxidativeStressMeasurement
    range: string
  input_sample:
    name: input_sample
    description: Description of input samples and manipulations
    from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
    exact_mappings:
    - OBI:0100051
    related_mappings:
    - OBI:0000747
    rank: 1000
    alias: input_sample
    owner: OxidativeStressMeasurement
    domain_of:
    - Measurement
    range: InputSample
  method_assay:
    name: method_assay
    description: The method or assay used
    from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
    exact_mappings:
    - OBI:0000070
    rank: 1000
    alias: method_assay
    owner: OxidativeStressMeasurement
    domain_of:
    - Measurement
    range: Assay
  protocol_notes:
    name: protocol_notes
    description: Protocol or SOP notes
    comments:
    - For EGFR signaling include cell type, receptor location in ALI culture, probe
      method, timing
    - For goblet cells include media type, species, disease state, donor age, exposure
      conditions
    - For mucin production include focus on secreted mucins not tethered to goblet
      cells
    from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
    related_mappings:
    - IAO:0000310
    broad_mappings:
    - OBI:0000272
    rank: 1000
    alias: protocol_notes
    owner: OxidativeStressMeasurement
    domain_of:
    - Measurement
    range: string
  id:
    name: id
    description: A unique identifier
    from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
    rank: 1000
    identifier: true
    alias: id
    owner: OxidativeStressMeasurement
    domain_of:
    - NamedEntity
    range: uriorcurie
    required: true
  description:
    name: description
    description: A detailed description
    from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
    rank: 1000
    alias: description
    owner: OxidativeStressMeasurement
    domain_of:
    - NamedEntity
    range: string