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Slot: Health-Layer Linkage (health_layer_linkage)

Downstream health-data-layer linkage hooks (OMOP, BDC, …) — see envar_health_layer. Optional: its members are Recommended/Optional, and the Core PHI assertion lives at the record root (phi_status).

Tier: recommended

Why this slot matters

Naming the downstream health-data layer (OMOP, BDC, …) and the join field makes the exposure record findable from the clinical side; without it the sidecar and the health records it serves drift apart, and the link must be reconstructed by hand.

In plain terms

Health studies keep patient data in large standard databases. This block notes which of those systems the exposure values were wired into and through which field, so someone browsing the health data can find their way back to this record.

URI: envar:slot/health_layer_linkage

Applicable Classes

Name Description Modifies Slot
EnvironmentalExposureRecord A single environmental-exposure record sidecar: the complete metadata graph t... no
DailyMaxTemperatureRecord Canonical record for daily maximum 2 m air temperature (Tmax) no
DailyMinTemperatureRecord Canonical record for daily minimum 2 m air temperature (Tmin) no
WetBulbGlobeTemperatureOutdoorRecord Canonical record for outdoor WBGT under the Liljegren 2008 formulation no
ExtremeHeatDayFlagRecord Canonical record for a daily binary extreme-heat-day flag, defined against a ... no

Properties

Type and Range

Property Value
Range HealthLayerLinkage
Domain Of EnvironmentalExposureRecord
Slot Group health_data_integration

Cardinality and Requirements

Property Value

Examples

Value
None

See Also

Identifier and Mapping Information

Annotations

property value
tier recommended
justification Naming the downstream health-data layer (OMOP, BDC, …) and the join field makes the exposure record findable from the clinical side; without it the sidecar and the health records it serves drift apart, and the link must be reconstructed by hand.
explanation Health studies keep patient data in large standard databases. This block notes which of those systems the exposure values were wired into and through which field, so someone browsing the health data can find their way back to this record.
covered_by None

Schema Source

Mappings

Mapping Type Mapped Value
self envar:health_layer_linkage
native envar:health_layer_linkage

LinkML Source

name: health_layer_linkage
annotations:
  tier:
    tag: tier
    value: recommended
  justification:
    tag: justification
    value: Naming the downstream health-data layer (OMOP, BDC, …) and the join field
      makes the exposure record findable from the clinical side; without it the sidecar
      and the health records it serves drift apart, and the link must be reconstructed
      by hand.
  explanation:
    tag: explanation
    value: Health studies keep patient data in large standard databases. This block
      notes which of those systems the exposure values were wired into and through
      which field, so someone browsing the health data can find their way back to
      this record.
  covered_by:
    tag: covered_by
    annotations:
      omop_gaia:
        tag: omop_gaia
        annotations:
          extent:
            tag: extent
            value: partial
          status:
            tag: status
            value: asserted
          where:
            tag: where
            value: external_exposure.exposure_source_value / exposure_concept_id +
              external_exposure.person_id
          note:
            tag: note
            value: 'Gaia lands values in OMOP external_exposure with a person link
              and a source-value hook, but names no explicit sidecar provenance-id
              join field. Conservative: partial.'
      degauss:
        tag: degauss
        annotations:
          extent:
            tag: extent
            value: absent
          status:
            tag: status
            value: asserted
          where:
            tag: where
            value: no column
          note:
            tag: note
            value: DeGAUSS appends geomarker columns to the cohort CSV but names no
              downstream health-layer target or join field.
      amadeus:
        tag: amadeus
        annotations:
          extent:
            tag: extent
            value: absent
          status:
            tag: status
            value: asserted
          where:
            tag: where
            value: no column
          note:
            tag: note
            value: Amadeus emits a data CSV with no downstream health-layer target
              or join field.
      cher:
        tag: cher
        annotations:
          extent:
            tag: extent
            value: partial
          status:
            tag: status
            value: asserted
          where:
            tag: where
            value: PostgreSQL schema=health + table_column_dictionary.reference_column_id
              (cross-table join to health resources)
          note:
            tag: note
            value: 'C-HER has a health schema and cross-table reference columns, but
              no sidecar-to-health-layer link-field declaration. Conservative: partial.'
      codata:
        tag: codata
        annotations:
          extent:
            tag: extent
            value: out_of_layer
          status:
            tag: status
            value: asserted
          where:
            tag: where
            value: no column
          note:
            tag: note
            value: Health-layer linkage hooks are instance/integration-layer; out
              of scope for CODATA.
description: 'Downstream health-data-layer linkage hooks (OMOP, BDC, …) — see envar_health_layer.
  Optional: its members are Recommended/Optional, and the Core PHI assertion lives
  at the record root (`phi_status`).'
title: Health-Layer Linkage
examples:
- description: abridged — see tests/data/valid/EnvironmentalExposureRecord-tmax_ideal.yaml
    for a full instance
  object:
    health_layer_target: omop_external_exposure
    health_layer_link_field: exposure_source_value
    cohort_size_anchored: 3
from_schema: https://w3id.org/linkml/microschemas/envar
see_also:
- https://ohdsi.github.io/CommonDataModel/
- https://biodatacatalyst.nhlbi.nih.gov/
rank: 1000
domain_of:
- EnvironmentalExposureRecord
slot_group: health_data_integration
range: HealthLayerLinkage
inlined: true