Class: BiomarkerDescriptor

A descriptor for biomarkers, bindable to NCIT

URI: dismech:class/BiomarkerDescriptor

 classDiagram
    class BiomarkerDescriptor
    click BiomarkerDescriptor href "../../classes/BiomarkerDescriptor/"
      Descriptor <|-- BiomarkerDescriptor
        click Descriptor href "../../classes/Descriptor/"

      BiomarkerDescriptor : clinical_course





        BiomarkerDescriptor --> "0..1" ClinicalCourseEnum : clinical_course
        click ClinicalCourseEnum href "../../enums/ClinicalCourseEnum/"



      BiomarkerDescriptor : description

      BiomarkerDescriptor : laterality





        BiomarkerDescriptor --> "0..1" LateralityEnum : laterality
        click LateralityEnum href "../../enums/LateralityEnum/"



      BiomarkerDescriptor : located_in





        BiomarkerDescriptor --> "0..1" AnatomicalEntityDescriptor : located_in
        click AnatomicalEntityDescriptor href "../../classes/AnatomicalEntityDescriptor/"



      BiomarkerDescriptor : modifier





        BiomarkerDescriptor --> "0..1" ModifierEnum : modifier
        click ModifierEnum href "../../enums/ModifierEnum/"



      BiomarkerDescriptor : onset





        BiomarkerDescriptor --> "0..1" OnsetDescriptor : onset
        click OnsetDescriptor href "../../classes/OnsetDescriptor/"



      BiomarkerDescriptor : preferred_term

      BiomarkerDescriptor : qualifiers





        BiomarkerDescriptor --> "*" Qualifier : qualifiers
        click Qualifier href "../../classes/Qualifier/"



      BiomarkerDescriptor : severity





        BiomarkerDescriptor --> "0..1" Any : severity
        click Any href "../../classes/Any/"



      BiomarkerDescriptor : spatial_extent





        BiomarkerDescriptor --> "0..1" SpatialExtentEnum : spatial_extent
        click SpatialExtentEnum href "../../enums/SpatialExtentEnum/"



      BiomarkerDescriptor : temporality





        BiomarkerDescriptor --> "0..1" TemporalityEnum : temporality
        click TemporalityEnum href "../../enums/TemporalityEnum/"



      BiomarkerDescriptor : term





        BiomarkerDescriptor --> "0..1 _recommended_" Term : term
        click Term href "../../classes/Term/"

Inheritance

• Descriptor
  • BiomarkerDescriptor

Slots

Name	Cardinality and Range	Description	Inheritance
preferred_term	1 String	The preferred human-readable term for this descriptor	Descriptor
description	0..1 String	A description of the descriptor	Descriptor
term	0..1 recommended Term	NCIT biomarker term reference	Descriptor
modifier	0..1 ModifierEnum	Directional or qualitative modifier for a descriptor (e	Descriptor
located_in	0..1 AnatomicalEntityDescriptor	Anatomical location where this entity/process occurs or procedure is performe...	Descriptor
laterality	0..1 LateralityEnum	Laterality qualifier (left, right, or bilateral)	Descriptor
spatial_extent	0..1 SpatialExtentEnum	The spatial extent or distribution pattern applicable to this descriptor (e	Descriptor
onset	0..1 OnsetDescriptor	Structured age of onset descriptor	Descriptor
temporality	0..1 TemporalityEnum	Temporal qualifier for this descriptor (e	Descriptor
clinical_course	0..1 ClinicalCourseEnum	Clinical course qualifier for this descriptor (e	Descriptor
severity	0..1 String or  Any or  SeverityQualifierEnum		Descriptor
qualifiers	* Qualifier	List of predicate-value pairs for formal post-composition	Descriptor

Usages

used by	used in	type	used
ExperimentalReadout	biomarker_term	range	BiomarkerDescriptor
Biochemical	biomarker_term	range	BiomarkerDescriptor

Identifier and Mapping Information

Schema Source

• from schema: https://w3id.org/monarch-initiative/dismech

Mappings

Mapping Type	Mapped Value
self	dismech:BiomarkerDescriptor
native	dismech:BiomarkerDescriptor

LinkML Source

Direct

name: BiomarkerDescriptor
description: A descriptor for biomarkers, bindable to NCIT
from_schema: https://w3id.org/monarch-initiative/dismech
is_a: Descriptor
slot_usage:
  term:
    name: term
    description: NCIT biomarker term reference
    bindings:
    - range: BiomarkerTerm
      obligation_level: REQUIRED
      binds_value_of: id

Induced

name: BiomarkerDescriptor
description: A descriptor for biomarkers, bindable to NCIT
from_schema: https://w3id.org/monarch-initiative/dismech
is_a: Descriptor
slot_usage:
  term:
    name: term
    description: NCIT biomarker term reference
    bindings:
    - range: BiomarkerTerm
      obligation_level: REQUIRED
      binds_value_of: id
attributes:
  preferred_term:
    name: preferred_term
    description: The preferred human-readable term for this descriptor. This may be
      more specific or nuanced than the linked ontology term label when the ontology
      does not fully capture the desired granularity. Note that postcomposition using
      the modifier slot may be appropriate for capturing the semantics of the preferred
      term.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: preferred_term
    owner: BiomarkerDescriptor
    domain_of:
    - Descriptor
    - ConditionDescriptor
    range: string
    required: true
  description:
    name: description
    description: A description of the descriptor. This may typically be redundant
      with the `term` object, but the description is more human-readable and may be
      used to communicate nuances not captured by the rigid standardization of the
      term object.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: description
    owner: BiomarkerDescriptor
    domain_of:
    - Descriptor
    - DietaryModification
    - GeneticContext
    - Dataset
    - ExperimentalModel
    - Experiment
    - ExperimentalPerturbation
    - ExperimentalReadout
    - ExperimentalControl
    - ClinicalTrial
    - ComputationalModel
    - ModelVariable
    - DifferentialDiagnosis
    - Subtype
    - CausalEdge
    - TreatmentMechanismTarget
    - ModelMechanismLink
    - BiomarkerReadout
    - SurrogateEndpointCollection
    - ProteinStructure
    - ExternalAssertion
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - HistopathologyFinding
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - AnimalModel
    - Treatment
    - InfectiousAgent
    - Transmission
    - Assay
    - Diagnosis
    - Inheritance
    - Variant
    - FunctionalEffect
    - Mechanism
    - ModelingConsideration
    - Definition
    - CriteriaSet
    - ConditionDescriptor
    - GOEnrichment
    - ComorbidityHypothesis
    - UpstreamConditionHypothesis
    - MechanisticHypothesis
    range: string
    recommended: false
  term:
    name: term
    description: NCIT biomarker term reference
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: term
    owner: BiomarkerDescriptor
    domain_of:
    - Descriptor
    - TermMapping
    - ConditionDescriptor
    - GOEnrichmentTerm
    range: Term
    bindings:
    - range: BiomarkerTerm
      obligation_level: REQUIRED
      binds_value_of: id
    recommended: true
    inlined: true
  modifier:
    name: modifier
    description: Directional or qualitative modifier for a descriptor (e.g., increased,
      decreased, abnormal)
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: modifier
    owner: BiomarkerDescriptor
    domain_of:
    - Descriptor
    range: ModifierEnum
  located_in:
    name: located_in
    description: Anatomical location where this entity/process occurs or procedure
      is performed
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: located_in
    owner: BiomarkerDescriptor
    domain_of:
    - Descriptor
    range: AnatomicalEntityDescriptor
    inlined: true
  laterality:
    name: laterality
    description: Laterality qualifier (left, right, or bilateral)
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: laterality
    owner: BiomarkerDescriptor
    domain_of:
    - Descriptor
    range: LateralityEnum
  spatial_extent:
    name: spatial_extent
    description: The spatial extent or distribution pattern applicable to this descriptor
      (e.g., focal, diffuse, extensive)
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: spatial_extent
    owner: BiomarkerDescriptor
    domain_of:
    - Descriptor
    range: SpatialExtentEnum
  onset:
    name: onset
    description: Structured age of onset descriptor. Combines an HPO onset category
      with optional quantitative age data (mean, min, max in years) and free-text
      notes.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: onset
    owner: BiomarkerDescriptor
    domain_of:
    - Descriptor
    - PhenotypeContext
    range: OnsetDescriptor
    inlined: true
  temporality:
    name: temporality
    description: Temporal qualifier for this descriptor (e.g., acute, chronic, recurrent)
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: temporality
    owner: BiomarkerDescriptor
    domain_of:
    - Descriptor
    range: TemporalityEnum
  clinical_course:
    name: clinical_course
    description: Clinical course qualifier for this descriptor (e.g., progressive,
      stable)
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: clinical_course
    owner: BiomarkerDescriptor
    domain_of:
    - Descriptor
    range: ClinicalCourseEnum
  severity:
    name: severity
    examples:
    - value: Severe
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: severity
    owner: BiomarkerDescriptor
    domain_of:
    - Descriptor
    - PhenotypeContext
    - Phenotype
    range: Any
    any_of:
    - range: SeverityQualifierEnum
    - range: string
  qualifiers:
    name: qualifiers
    description: List of predicate-value pairs for formal post-composition. Allows
      OWL-like expressivity with controlled predicates (e.g., RO relations) and values.
    deprecated: Prefer explicit slots like located_in and laterality instead of generic
      qualifiers
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: qualifiers
    owner: BiomarkerDescriptor
    domain_of:
    - Descriptor
    range: Qualifier
    multivalued: true
    inlined: true
    inlined_as_list: true