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Class: Biochemical

URI: dismech:Biochemical

 classDiagram
    class Biochemical
    click Biochemical href "../Biochemical/"
      Biochemical : assays





        Biochemical --> "*" AssayDescriptor : assays
        click AssayDescriptor href "../AssayDescriptor/"



      Biochemical : biomarker_term





        Biochemical --> "0..1" BiomarkerDescriptor : biomarker_term
        click BiomarkerDescriptor href "../BiomarkerDescriptor/"



      Biochemical : cell_types





        Biochemical --> "*" CellTypeDescriptor : cell_types
        click CellTypeDescriptor href "../CellTypeDescriptor/"



      Biochemical : context

      Biochemical : evidence





        Biochemical --> "*" EvidenceItem : evidence
        click EvidenceItem href "../EvidenceItem/"



      Biochemical : frequency





        Biochemical --> "0..1" Any : frequency
        click Any href "../Any/"



      Biochemical : name

      Biochemical : notes

      Biochemical : presence

      Biochemical : specificity

      Biochemical : subtype

      Biochemical : synonyms

Slots

Name Cardinality and Range Description Inheritance
name 1
String		 direct
biomarker_term 0..1
BiomarkerDescriptor		 Ontology term for a biomarker (from NCIT) direct
presence 0..1
String		 direct
evidence * recommended
EvidenceItem		 direct
specificity 0..1
String		 direct
frequency 0..1
Any or 
FrequencyEnum or 
FrequencyQuantity		 direct
notes 0..1
String		 direct
context 0..1
String		 direct
subtype 0..1
String		 direct
cell_types *
CellTypeDescriptor		 direct
assays *
AssayDescriptor		 direct
synonyms *
String		 direct

Usages

used by used in type used
Disease biochemical range Biochemical

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Biochemical
from_schema: https://w3id.org/monarch-initiative/dismech
slots:
- name
- biomarker_term
- presence
- evidence
- specificity
- frequency
- notes
- context
- subtype
- cell_types
- assays
- synonyms

Induced

name: Biochemical
from_schema: https://w3id.org/monarch-initiative/dismech
attributes:
  name:
    name: name
    examples:
    - value: Adolescent Nephronophthisis
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    identifier: true
    alias: name
    owner: Biochemical
    domain_of:
    - ClinicalTrial
    - ComputationalModel
    - DifferentialDiagnosis
    - Subtype
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - Genetic
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycleStage
    - Treatment
    - InfectiousAgent
    - Transmission
    - Assay
    - Diagnosis
    - Inheritance
    - Variant
    - Mechanism
    - ModelingConsideration
    - Definition
    - CriteriaSet
    - ComorbidityAssociation
    range: string
    required: true
  biomarker_term:
    name: biomarker_term
    description: Ontology term for a biomarker (from NCIT)
    comments:
    - Use NCIT terms for biomarkers (proteins, genes, fusion products)
    - NCIT:C16342 (Biomarker) is the root class for validation
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: biomarker_term
    owner: Biochemical
    domain_of:
    - Biochemical
    range: BiomarkerDescriptor
    inlined: true
  presence:
    name: presence
    examples:
    - value: Positive
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: presence
    owner: Biochemical
    domain_of:
    - Biochemical
    - Genetic
    - Environmental
    - Diagnosis
    range: string
  evidence:
    name: evidence
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: evidence
    owner: Biochemical
    domain_of:
    - PhenotypeContext
    - Dataset
    - ClinicalTrial
    - ComputationalModel
    - DifferentialDiagnosis
    - Subtype
    - CausalEdge
    - TreatmentMechanismTarget
    - Finding
    - Prevalence
    - ProgressionInfo
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - Genetic
    - Environmental
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - AnimalModel
    - Treatment
    - InfectiousAgent
    - Transmission
    - Diagnosis
    - Inheritance
    - Variant
    - ModelingConsideration
    - ClassificationAssignment
    - Definition
    - CriteriaSet
    - AssociationSignal
    - AssociationStatistics
    - ComorbidityHypothesis
    - UpstreamConditionHypothesis
    - MechanisticHypothesis
    range: EvidenceItem
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  specificity:
    name: specificity
    examples:
    - value: High
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: specificity
    owner: Biochemical
    domain_of:
    - Biochemical
    range: string
  frequency:
    name: frequency
    examples:
    - value: Occasional
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: frequency
    owner: Biochemical
    domain_of:
    - PhenotypeContext
    - Pathophysiology
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - Genetic
    range: Any
    any_of:
    - range: FrequencyEnum
    - range: FrequencyQuantity
  notes:
    name: notes
    examples:
    - value: Contagious stage where symptoms appear and the bacteria can be spread
        to others.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: notes
    owner: Biochemical
    domain_of:
    - GeneticContext
    - OnsetDescriptor
    - PhenotypeContext
    - Dataset
    - ClinicalTrial
    - ComputationalModel
    - DifferentialDiagnosis
    - Prevalence
    - ProgressionInfo
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - Genetic
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - Treatment
    - Transmission
    - Diagnosis
    - ClassificationAssignment
    - Definition
    - CriteriaSet
    - TermMapping
    - MappingConsistency
    - ComorbidityAssociation
    - AssociationSignal
    - AssociationMetric
    - AssociationStatistics
    - MechanisticHypothesis
    range: string
  context:
    name: context
    examples:
    - value: Pregnancy
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: context
    owner: Biochemical
    domain_of:
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - Treatment
    range: string
  subtype:
    name: subtype
    examples:
    - value: Eyelid Myoclonia with Absences
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: subtype
    owner: Biochemical
    domain_of:
    - PhenotypeContext
    - Prevalence
    - ProgressionInfo
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - Genetic
    range: string
  cell_types:
    name: cell_types
    examples:
    - value: '[{preferred_term: Macrophage}, {preferred_term: T Cell}]'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: cell_types
    owner: Biochemical
    domain_of:
    - Pathophysiology
    - Biochemical
    range: CellTypeDescriptor
    multivalued: true
    inlined: true
    inlined_as_list: true
  assays:
    name: assays
    examples:
    - value: '[{preferred_term: Elevated Blood Glucose}]'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: assays
    owner: Biochemical
    domain_of:
    - Pathophysiology
    - Biochemical
    range: AssayDescriptor
    multivalued: true
    inlined: true
    inlined_as_list: true
  synonyms:
    name: synonyms
    examples:
    - value: '[''CYFRA 21-1'']'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: synonyms
    owner: Biochemical
    domain_of:
    - Pathophysiology
    - Biochemical
    - Environmental
    - Disease
    - Variant
    range: string
    multivalued: true