Class: BALFSputumOutput

Measurement results from a BALF/sputum assay. Contains inflammatory cell differentials, cytokine concentrations, and microbiome metrics.

URI: soma:BALFSputumOutput

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

      BALFSputumOutput : alpha_diversity





        BALFSputumOutput --> "0..1" QuantityValue : alpha_diversity
        click QuantityValue href "../QuantityValue/"



      BALFSputumOutput : bacterial_load





        BALFSputumOutput --> "0..1" QuantityValue : bacterial_load
        click QuantityValue href "../QuantityValue/"



      BALFSputumOutput : beta_diversity





        BALFSputumOutput --> "0..1" QuantityValue : beta_diversity
        click QuantityValue href "../QuantityValue/"



      BALFSputumOutput : cell_free_dna





        BALFSputumOutput --> "0..1" QuantityValue : cell_free_dna
        click QuantityValue href "../QuantityValue/"



      BALFSputumOutput : description

      BALFSputumOutput : eosinophil_percentage





        BALFSputumOutput --> "0..1" QuantityValue : eosinophil_percentage
        click QuantityValue href "../QuantityValue/"



      BALFSputumOutput : id

      BALFSputumOutput : il1_beta_concentration





        BALFSputumOutput --> "0..1" QuantityValue : il1_beta_concentration
        click QuantityValue href "../QuantityValue/"



      BALFSputumOutput : il6_concentration





        BALFSputumOutput --> "0..1" QuantityValue : il6_concentration
        click QuantityValue href "../QuantityValue/"



      BALFSputumOutput : il8_concentration





        BALFSputumOutput --> "0..1" QuantityValue : il8_concentration
        click QuantityValue href "../QuantityValue/"



      BALFSputumOutput : lymphocyte_percentage





        BALFSputumOutput --> "0..1" QuantityValue : lymphocyte_percentage
        click QuantityValue href "../QuantityValue/"



      BALFSputumOutput : macrophage_percentage





        BALFSputumOutput --> "0..1" QuantityValue : macrophage_percentage
        click QuantityValue href "../QuantityValue/"



      BALFSputumOutput : name

      BALFSputumOutput : neutrophil_percentage





        BALFSputumOutput --> "0..1" QuantityValue : neutrophil_percentage
        click QuantityValue href "../QuantityValue/"



      BALFSputumOutput : tnf_alpha_concentration





        BALFSputumOutput --> "0..1" QuantityValue : tnf_alpha_concentration
        click QuantityValue href "../QuantityValue/"



      BALFSputumOutput : total_cell_count





        BALFSputumOutput --> "0..1" QuantityValue : total_cell_count
        click QuantityValue href "../QuantityValue/"



      BALFSputumOutput : total_protein_concentration





        BALFSputumOutput --> "0..1" QuantityValue : total_protein_concentration
        click QuantityValue href "../QuantityValue/"

Inheritance

NamedThing
- AssayOutputMeasurement
  - BALFSputumOutput

Slots

Name	Cardinality and Range	Description	Inheritance
neutrophil_percentage	0..1 QuantityValue	Neutrophil percentage in BALF/sputum	direct
eosinophil_percentage	0..1 QuantityValue	Eosinophil percentage in BALF/sputum	direct
macrophage_percentage	0..1 QuantityValue	Macrophage percentage in BALF/sputum	direct
lymphocyte_percentage	0..1 QuantityValue	Lymphocyte percentage in BALF/sputum	direct
total_cell_count	0..1 QuantityValue	Total cell count in BALF/sputum	direct
il6_concentration	0..1 QuantityValue	IL-6 concentration	direct
il8_concentration	0..1 QuantityValue	IL-8 concentration	direct
tnf_alpha_concentration	0..1 QuantityValue	TNF-alpha concentration	direct
il1_beta_concentration	0..1 QuantityValue	IL-1 beta concentration	direct
total_protein_concentration	0..1 QuantityValue	Total protein concentration	direct
alpha_diversity	0..1 QuantityValue	Alpha diversity (microbiome)	direct
beta_diversity	0..1 QuantityValue	Beta diversity (microbiome)	direct
bacterial_load	0..1 QuantityValue	Bacterial load (16S copies or CFU)	direct
cell_free_dna	0..1 QuantityValue	Cell-free DNA concentration	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
BALFSputumAssay	has_specified_output	range	BALFSputumOutput

Identifier and Mapping Information

Schema Source

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

Mappings

Mapping Type	Mapped Value
self	soma:BALFSputumOutput
native	soma:BALFSputumOutput

LinkML Source

Direct

name: BALFSputumOutput
description: Measurement results from a BALF/sputum assay. Contains inflammatory cell
  differentials, cytokine concentrations, and microbiome metrics.
from_schema: https://w3id.org/EHS-Data-Standards/soma
is_a: AssayOutputMeasurement
slots:
- neutrophil_percentage
- eosinophil_percentage
- macrophage_percentage
- lymphocyte_percentage
- total_cell_count
- il6_concentration
- il8_concentration
- tnf_alpha_concentration
- il1_beta_concentration
- total_protein_concentration
- alpha_diversity
- beta_diversity
- bacterial_load
- cell_free_dna

Induced

name: BALFSputumOutput
description: Measurement results from a BALF/sputum assay. Contains inflammatory cell
  differentials, cytokine concentrations, and microbiome metrics.
from_schema: https://w3id.org/EHS-Data-Standards/soma
is_a: AssayOutputMeasurement
attributes:
  neutrophil_percentage:
    name: neutrophil_percentage
    description: Neutrophil percentage in BALF/sputum.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: neutrophil_percentage
    owner: BALFSputumOutput
    domain_of:
    - BALFSputumOutput
    range: QuantityValue
    inlined: true
  eosinophil_percentage:
    name: eosinophil_percentage
    description: Eosinophil percentage in BALF/sputum.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: eosinophil_percentage
    owner: BALFSputumOutput
    domain_of:
    - BALFSputumOutput
    range: QuantityValue
    inlined: true
  macrophage_percentage:
    name: macrophage_percentage
    description: Macrophage percentage in BALF/sputum.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: macrophage_percentage
    owner: BALFSputumOutput
    domain_of:
    - BALFSputumOutput
    range: QuantityValue
    inlined: true
  lymphocyte_percentage:
    name: lymphocyte_percentage
    description: Lymphocyte percentage in BALF/sputum.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: lymphocyte_percentage
    owner: BALFSputumOutput
    domain_of:
    - BALFSputumOutput
    range: QuantityValue
    inlined: true
  total_cell_count:
    name: total_cell_count
    description: Total cell count in BALF/sputum.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: total_cell_count
    owner: BALFSputumOutput
    domain_of:
    - BALFSputumOutput
    range: QuantityValue
    inlined: true
  il6_concentration:
    name: il6_concentration
    description: IL-6 concentration.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: il6_concentration
    owner: BALFSputumOutput
    domain_of:
    - BALFSputumOutput
    range: QuantityValue
    inlined: true
  il8_concentration:
    name: il8_concentration
    description: IL-8 concentration.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: il8_concentration
    owner: BALFSputumOutput
    domain_of:
    - BALFSputumOutput
    range: QuantityValue
    inlined: true
  tnf_alpha_concentration:
    name: tnf_alpha_concentration
    description: TNF-alpha concentration.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: tnf_alpha_concentration
    owner: BALFSputumOutput
    domain_of:
    - BALFSputumOutput
    range: QuantityValue
    inlined: true
  il1_beta_concentration:
    name: il1_beta_concentration
    description: IL-1 beta concentration.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: il1_beta_concentration
    owner: BALFSputumOutput
    domain_of:
    - BALFSputumOutput
    range: QuantityValue
    inlined: true
  total_protein_concentration:
    name: total_protein_concentration
    description: Total protein concentration.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: total_protein_concentration
    owner: BALFSputumOutput
    domain_of:
    - BALFSputumOutput
    range: QuantityValue
    inlined: true
  alpha_diversity:
    name: alpha_diversity
    description: Alpha diversity (microbiome).
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: alpha_diversity
    owner: BALFSputumOutput
    domain_of:
    - BALFSputumOutput
    range: QuantityValue
    inlined: true
  beta_diversity:
    name: beta_diversity
    description: Beta diversity (microbiome).
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: beta_diversity
    owner: BALFSputumOutput
    domain_of:
    - BALFSputumOutput
    range: QuantityValue
    inlined: true
  bacterial_load:
    name: bacterial_load
    description: Bacterial load (16S copies or CFU).
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: bacterial_load
    owner: BALFSputumOutput
    domain_of:
    - BALFSputumOutput
    range: QuantityValue
    inlined: true
  cell_free_dna:
    name: cell_free_dna
    description: Cell-free DNA concentration.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: cell_free_dna
    owner: BALFSputumOutput
    domain_of:
    - BALFSputumOutput
    range: QuantityValue
    inlined: true
  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: BALFSputumOutput
    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: BALFSputumOutput
    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: BALFSputumOutput
    domain_of:
    - NamedThing
    range: string