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Class: AssociationSignal

An association signal from EHR, registry, or computational sources, optionally stratified by sex, age, or cohort.

URI: dismech:AssociationSignal

 classDiagram
    class AssociationSignal
    click AssociationSignal href "../AssociationSignal/"
      AssociationSignal : a_before_b

      AssociationSignal : b_before_a

      AssociationSignal : demographics





        AssociationSignal --> "0..1" Demographics : demographics
        click Demographics href "../Demographics/"



      AssociationSignal : directionality





        AssociationSignal --> "0..1" ComorbidityDirectionEnum : directionality
        click ComorbidityDirectionEnum href "../ComorbidityDirectionEnum/"



      AssociationSignal : disorder_a_count

      AssociationSignal : disorder_b_count

      AssociationSignal : evidence





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



      AssociationSignal : go_enrichment





        AssociationSignal --> "0..1" GOEnrichment : go_enrichment
        click GOEnrichment href "../GOEnrichment/"



      AssociationSignal : limited_precision

      AssociationSignal : mapping_notes

      AssociationSignal : method





        AssociationSignal --> "0..1" AssociationSignalMethodEnum : method
        click AssociationSignalMethodEnum href "../AssociationSignalMethodEnum/"



      AssociationSignal : metrics





        AssociationSignal --> "*" AssociationMetric : metrics
        click AssociationMetric href "../AssociationMetric/"



      AssociationSignal : notes

      AssociationSignal : pair_count

      AssociationSignal : population

      AssociationSignal : precision_count_threshold

      AssociationSignal : same_time

      AssociationSignal : signal_disorder_a_id

      AssociationSignal : signal_disorder_b_id

      AssociationSignal : source





        AssociationSignal --> "0..1" AssociationSignalSourceEnum : source
        click AssociationSignalSourceEnum href "../AssociationSignalSourceEnum/"



      AssociationSignal : statistics





        AssociationSignal --> "0..1" AssociationStatistics : statistics
        click AssociationStatistics href "../AssociationStatistics/"

Slots

Name Cardinality and Range Description Inheritance
source 0..1
AssociationSignalSourceEnum		 Source dataset or provenance label direct
method 0..1
AssociationSignalMethodEnum		 Method or pipeline name direct
signal_disorder_a_id 0..1
Uriorcurie		 Original identifier for disorder A in this signal (CURIE, e direct
signal_disorder_b_id 0..1
Uriorcurie		 Original identifier for disorder B in this signal (CURIE, e direct
population 0..1
String		 Population or cohort description (e direct
demographics 0..1
Demographics		 Demographic stratification for an association signal direct
mapping_notes 0..1
String		 Notes on code-to-concept mapping decisions for this signal direct
disorder_a_count 0..1
Integer		 Number of records/patients carrying disorder A in the source dataset direct
disorder_b_count 0..1
Integer		 Number of records/patients carrying disorder B in the source dataset direct
pair_count 0..1
Integer		 Number of records/patients with co-occurrence of disorder A and disorder B in... direct
limited_precision 0..1
Boolean		 Whether the signal has limited statistical precision due to small co-occurren... direct
precision_count_threshold 0..1
Integer		 Co-occurrence count threshold used to flag limited precision direct
directionality 0..1
ComorbidityDirectionEnum		 Direction of a comorbidity/trajectory association direct
a_before_b 0..1
Float		 Probability or fraction of A before B in an EHR signal direct
b_before_a 0..1
Float		 Probability or fraction of B before A in an EHR signal direct
same_time 0..1
Float		 Probability or fraction of A and B occurring in the same time window direct
metrics *
AssociationMetric		 Quantitative association metrics direct
statistics 0..1
AssociationStatistics		 Statistical summary for an association signal direct
go_enrichment 0..1
GOEnrichment		 GO enrichment results associated with a signal direct
evidence * recommended
EvidenceItem		 direct
notes 0..1
String		 direct

Usages

used by used in type used
ComorbidityAssociation association_signals range AssociationSignal

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: AssociationSignal
description: An association signal from EHR, registry, or computational sources, optionally
  stratified by sex, age, or cohort.
from_schema: https://w3id.org/monarch-initiative/dismech
slots:
- source
- method
- signal_disorder_a_id
- signal_disorder_b_id
- population
- demographics
- mapping_notes
- disorder_a_count
- disorder_b_count
- pair_count
- limited_precision
- precision_count_threshold
- directionality
- a_before_b
- b_before_a
- same_time
- metrics
- statistics
- go_enrichment
- evidence
- notes
slot_usage:
  source:
    name: source
    range: AssociationSignalSourceEnum
  method:
    name: method
    range: AssociationSignalMethodEnum

Induced

name: AssociationSignal
description: An association signal from EHR, registry, or computational sources, optionally
  stratified by sex, age, or cohort.
from_schema: https://w3id.org/monarch-initiative/dismech
slot_usage:
  source:
    name: source
    range: AssociationSignalSourceEnum
  method:
    name: method
    range: AssociationSignalMethodEnum
attributes:
  source:
    name: source
    description: Source dataset or provenance label
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: source
    owner: AssociationSignal
    domain_of:
    - AssociationSignal
    range: AssociationSignalSourceEnum
  method:
    name: method
    description: Method or pipeline name
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: method
    owner: AssociationSignal
    domain_of:
    - AssociationSignal
    - GOEnrichment
    range: AssociationSignalMethodEnum
  signal_disorder_a_id:
    name: signal_disorder_a_id
    description: Original identifier for disorder A in this signal (CURIE, e.g., ICD10:E12)
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: signal_disorder_a_id
    owner: AssociationSignal
    domain_of:
    - AssociationSignal
    range: uriorcurie
  signal_disorder_b_id:
    name: signal_disorder_b_id
    description: Original identifier for disorder B in this signal (CURIE, e.g., ICD10:L28)
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: signal_disorder_b_id
    owner: AssociationSignal
    domain_of:
    - AssociationSignal
    range: uriorcurie
  population:
    name: population
    description: Population or cohort description (e.g., for prevalence or association
      signals)
    examples:
    - value: Global
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: population
    owner: AssociationSignal
    domain_of:
    - PhenotypeContext
    - Prevalence
    - AssociationSignal
    range: string
  demographics:
    name: demographics
    description: Demographic stratification for an association signal
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: demographics
    owner: AssociationSignal
    domain_of:
    - AssociationSignal
    range: Demographics
    inlined: true
  mapping_notes:
    name: mapping_notes
    description: Notes on code-to-concept mapping decisions for this signal
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: mapping_notes
    owner: AssociationSignal
    domain_of:
    - AssociationSignal
    range: string
  disorder_a_count:
    name: disorder_a_count
    description: Number of records/patients carrying disorder A in the source dataset
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: disorder_a_count
    owner: AssociationSignal
    domain_of:
    - AssociationSignal
    range: integer
  disorder_b_count:
    name: disorder_b_count
    description: Number of records/patients carrying disorder B in the source dataset
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: disorder_b_count
    owner: AssociationSignal
    domain_of:
    - AssociationSignal
    range: integer
  pair_count:
    name: pair_count
    description: Number of records/patients with co-occurrence of disorder A and disorder
      B in the source dataset
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: pair_count
    owner: AssociationSignal
    domain_of:
    - AssociationSignal
    range: integer
  limited_precision:
    name: limited_precision
    description: Whether the signal has limited statistical precision due to small
      co-occurrence count
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: limited_precision
    owner: AssociationSignal
    domain_of:
    - AssociationSignal
    range: boolean
  precision_count_threshold:
    name: precision_count_threshold
    description: Co-occurrence count threshold used to flag limited precision
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: precision_count_threshold
    owner: AssociationSignal
    domain_of:
    - AssociationSignal
    range: integer
  directionality:
    name: directionality
    description: Direction of a comorbidity/trajectory association
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: directionality
    owner: AssociationSignal
    domain_of:
    - ComorbidityAssociation
    - AssociationSignal
    range: ComorbidityDirectionEnum
  a_before_b:
    name: a_before_b
    description: Probability or fraction of A before B in an EHR signal
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: a_before_b
    owner: AssociationSignal
    domain_of:
    - AssociationSignal
    range: float
  b_before_a:
    name: b_before_a
    description: Probability or fraction of B before A in an EHR signal
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: b_before_a
    owner: AssociationSignal
    domain_of:
    - AssociationSignal
    range: float
  same_time:
    name: same_time
    description: Probability or fraction of A and B occurring in the same time window
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: same_time
    owner: AssociationSignal
    domain_of:
    - AssociationSignal
    range: float
  metrics:
    name: metrics
    description: Quantitative association metrics
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: metrics
    owner: AssociationSignal
    domain_of:
    - AssociationSignal
    - AssociationStatistics
    range: AssociationMetric
    multivalued: true
    inlined: true
    inlined_as_list: true
  statistics:
    name: statistics
    description: Statistical summary for an association signal
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: statistics
    owner: AssociationSignal
    domain_of:
    - AssociationSignal
    range: AssociationStatistics
    inlined: true
  go_enrichment:
    name: go_enrichment
    description: GO enrichment results associated with a signal
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: go_enrichment
    owner: AssociationSignal
    domain_of:
    - AssociationSignal
    range: GOEnrichment
    inlined: true
  evidence:
    name: evidence
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: evidence
    owner: AssociationSignal
    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
  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: AssociationSignal
    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