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EnVar microschemas · class atlas

EnVar Microschemas — Umbrella Schema

LinkML microschemas for environmental exposure variables (EnVar). Initial scope: heat-related exposures (Tmax, WBGT, heat index, heat-wave flags) and the surrounding provenance metadata needed to load them into OMOP external_exposure with full reproducibility…

The composite record · EnvironmentalExposureRecord Environmental Exposure Record A single environmental-exposure record sidecar: the complete metadata graph t...

Concrete record subclasses pre-wired for a specific variable — the shapes a workshop dataset actually instantiates.

Full element index — every class, enum, type & slot

Classes

Class Description
AnyValue An arbitrary passthrough object (open-ended key/value map) whose keys are not...
CodedValue A value from a controlled vocabulary
DataLayout How the companion data file (CSV / parquet) is laid out and how this record's...
DepositMetadata Deposit-time slots required when the sidecar travels alongside a published FA...
DerivedHeatMetric Methodology slots specific to derived heat metrics (WBGT, Heat Index, UTCI, a...
EnvironmentalExposureRecord A single environmental-exposure record sidecar: the complete metadata graph t...
        DailyMaxTemperatureRecord Canonical record for daily maximum 2 m air temperature (Tmax)
        DailyMinTemperatureRecord Canonical record for daily minimum 2 m air temperature (Tmin)
        ExtremeHeatDayFlagRecord Canonical record for a daily binary extreme-heat-day flag, defined against a ...
        WetBulbGlobeTemperatureOutdoorRecord Canonical record for outdoor WBGT under the Liljegren 2008 formulation
EquationInput A single physical-state input to a derived heat metric, recorded as a typed r...
ExposureModel The model class that produced the values (interpolation, reanalysis, ML, stat...
HealthLayerLinkage Hooks the sidecar uses to be findable from a downstream health-data layer (OM...
LinkageMethod How a gridded environmental value gets attached to a patient: the resolution ...
MicroschemaDefinition A metaclass for classes that conform to the Microschema profile
ModelAggregateUncertainty Whole-model uncertainty summary — cross-validation metrics and the reference ...
ProvenanceChain The ordered list of all upstream ToolRuns whose outputs were inputs to this...
Quantity A numerical value with unit
SourceDataset The upstream gridded / station product the exposure values originate from
SpatialReference Spatial provenance of an environmental exposure value: the native grid / foot...
TemporalReference Temporal provenance of an environmental exposure value: native temporal grain...
TimeInterval A period between two timepoints
Timepoint A point in time, potentially relative
ToolRun A single tool invocation that produced an output from one or more inputs: too...
Uncertainty Uncertainty and quality character of a value series: per-value uncertainty ty...
ValueMicroschemaDefinition A microschema representing a typed value with optional unit/system
VariableIdentity The identity and semantics of an environmental exposure variable — what physi...

Enumerations

Enumeration Description
AddressPeriodAlignmentEnum How the patient's location-over-time (the spatial axis of trajectory resoluti...
BiasCorrectionAppliedEnum Whether and how bias correction has been applied
BufferAggregationEnum Aggregation within a buffer
CalendarEnum Calendar of the time axis
ClinicalDateAssignmentEnum The clinical-side mirror of DayBoundaryConventionEnum (envar_temporal): whi...
ComparatorEnum Comparator for quantity values
ConceptStatusEnum Status of a variable's representation in the target health-data vocabulary na...
DataTypeEnum The data type of an exposure value
DayBoundaryConventionEnum Where the 24-hour day window starts
DepositRepositoryEnum Repository hosting a FAIR deposit
EquationVariantEnum Equation variant for a derived heat metric
ExposureModelTypeEnum The class of model that produced the values
ExtractionMethodEnum How a gridded value was extracted at a target location
GeocodingPrecisionEnum Geocoder precision category, mirroring DeGAUSS `geocoder
HealthLayerTargetEnum The downstream health-data layer a sidecar links into
HeatMetricFamilyEnum Family of heat metric
HeatWaveThresholdDefinitionEnum How the heat-wave threshold is defined
HomogenisationStatusEnum For station-based products, the homogenisation status of values across the re...
IndoorOutdoorEnum Indoor / outdoor regime for derived heat metrics
LagAlignmentEnum Whether the values have been pre-aligned to a clinical event window in this E...
LinkageStrategyEnum The spatial rule used to read an environmental value out of the exposure surf...
MissingDataHandlingEnum How the source handles missing values
MissingReasonEnum Controlled reasons that a slot value is missing
NullSemanticsEnum The kind of "missing or zero" a per-value cell carries
PartialDayAttributionEnum How boundary / transition days of the patient's trajectory (trip start / end,...
PhiStatusEnum PHI content of the sidecar
PrivacyTransformationEnum A privacy-protecting transformation applied to a linked location after the sp...
ProvenanceChainTerminusEnum The kind of root of a provenance chain
SolarRadiationBasisEnum Basis used for the solar-radiation input to a heat metric
SourceNativeFormatEnum Format the source ships in
SpatialAggregationPreservationEnum The quantity a spatial-aggregation operator holds invariant when a value is r...
TableOrientationEnum How variables map onto columns in the companion data file
TargetGeographyTypeEnum Geographic unit the exposure is attached to
TemporalAggregationMethodEnum How sub-period values were aggregated
TemporalResolutionEnum Native temporal grain of the source product
UncertaintyTypeEnum Kind of per-value uncertainty

Types

Type Description
Boolean A binary (true or false) value
Curie a compact URI
Date a date (year, month and day) in an idealized calendar
DateOrDatetime Either a date or a datetime
Datetime The combination of a date and time
Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci...
Double A real number that conforms to the xsd:double specification
Float A real number that conforms to the xsd:float specification
Integer An integer
Jsonpath A string encoding a JSON Path
Jsonpointer A string encoding a JSON Pointer
Ncname Prefix part of CURIE
Nodeidentifier A URI, CURIE or BNODE that represents a node in a model
Objectidentifier A URI or CURIE that represents an object in the model
Sparqlpath A string encoding a SPARQL Property Path
String A character string
Time A time object represents a (local) time of day, independent of any particular...
Uri a complete URI
Uriorcurie a URI or a CURIE

Slots

Slot Description
address_period_alignment How the patient's location-over-time (the spatial axis of trajectory resoluti...
bias_correction_applied Whether and how bias correction has been applied
bias_correction_applied_missing_reason Reason bias_correction_applied is null
calendar Calendar of the time axis
cf_cell_methods CF cell_methods string describing how the value summarises sub-period value...
chain_compatibility_assertions Declarations that two chain steps are compatible (e
clinical_date_assignment_convention The clinical-side mirror of day_boundary_convention (envar_temporal): which...
clinical_date_assignment_convention_missing_reason Reason clinical_date_assignment_convention is null
code The code value as a CURIE
code_label Human-readable label for the code
code_system The code system URI
cohort_size_anchored Number of distinct persons this exposure record was extracted for
cohort_size_anchored_missing_reason Reason cohort_size_anchored is null
comparator Comparison operator (less than, greater than, etc
concept_mappings Cross-references binding this variable to other vocabularies and ontologies, ...
concept_status Status of this variable's coverage in the target health-data vocabulary (`exi...
container_image_digest SHA256 of the container image actually used (not just the tag)
container_image_digest_missing_reason Reason container_image_digest is null
container_image_repository Container image repository, e
container_image_repository_missing_reason Reason container_image_repository is null
crs Coordinate reference system as an EPSG identifier or PROJ string
cv_r2 Cross-validated R² for the model as a whole
cv_rmse Cross-validated RMSE for the model as a whole
data_completeness_pct Percent of (location, date) cells in the extracted window that have a non-mis...
data_completeness_pct_missing_reason Reason data_completeness_pct is null
data_layout Data-layout object binding this sidecar to the columns of the companion data ...
dataset_and_provenance Where the values live and come from — the companion file's column layout, the...
datetime Absolute timestamp
day_boundary_convention Where the 24-hour day window starts
dcat_distribution_url DCAT-compatible distribution URL for catalogue integration
dcat_distribution_url_missing_reason Reason dcat_distribution_url is null
deposit_doi DOI assigned by the deposit repository (e
deposit_doi_missing_reason Reason deposit_doi is null (e
deposit_license_spdx SPDX identifier of the license under which the derived exposure record (not...
deposit_metadata FAIR-deposit metadata, present when the sidecar is intended to travel with a ...
deposit_redistribution_constraints_inherited Constraints from any input source that pass through to the deposit
deposit_repository Repository hosting the deposit
deposit_repository_missing_reason Reason deposit_repository is null
derived_heat_metric Heat-metric methodology, present when the variable is a derived heat metric —...
domain_of_use Domains where this microschema is applicable
duration Duration as alternative to start/end
equation_inputs Typed per-input references for a multi-input derived metric (Heat Index from ...
equation_validity_range Validity-range conditions for the equation, serialised as a JSON string
equation_validity_range_missing_reason Reason equation_validity_range is null
equation_variant For derived heat metrics, the equation variant used
equation_variant_missing_reason Reason equation_variant is null
exposure_description What was measured, for whom, where, when, and how — the generic scientific an...
exposure_model The exposure-model object describing how values were produced
exposure_model_cross_validation_r2 Model cross-validation R², where reported by the producer
exposure_model_cross_validation_r2_missing_reason Reason exposure_model_cross_validation_r2 is null
exposure_model_ensemble_member_count For ensemble products, the number of members
exposure_model_ensemble_member_count_missing_reason Reason exposure_model_ensemble_member_count is null
exposure_model_inputs Inputs to the model
exposure_model_known_biases Free-text flags of known issues, e
exposure_model_paper_doi DOI of the methods paper describing the model (Thornton et al
exposure_model_paper_doi_missing_reason Reason exposure_model_paper_doi is null
exposure_model_type The class of model that produced the values
extraction_buffer_m Radius of any spatial buffer applied (e
extraction_buffer_m_missing_reason Reason extraction_buffer_m is null
extraction_method How a gridded value was extracted at the patient's coordinates
extraction_window_end Actual end date the run extracted
extraction_window_start Actual start date the run extracted
geocoding_precision_propagated Quality category propagated from the upstream geocoder (DeGAUSS precision c...
geocoding_score_propagated Geocoder score (0-1) propagated from the upstream geocoder so the exposure re...
geocoding_score_propagated_missing_reason Reason geocoding_score_propagated is null
health_data_integration How the record meets patient data and travels onward — the gridded-to-patient...
health_layer_link_field Name of the field in the target health-data layer that carries `provenance_id...
health_layer_linkage Downstream health-data-layer linkage hooks (OMOP, BDC, …) — see envar_health_...
health_layer_target The downstream health-data layer this sidecar links into
heat_metric_family The family of heat metric this variable represents
heat_wave_min_consecutive_days Minimum-consecutive-days rule for heat-wave flags (commonly 2 or 3)
heat_wave_min_consecutive_days_missing_reason Reason heat_wave_min_consecutive_days is null
heat_wave_threshold_definition For heat-wave flags, the definition of the threshold (absolute, percentile-lo...
heat_wave_threshold_definition_missing_reason Reason heat_wave_threshold_definition is null
heat_wave_threshold_specifier Free-form specifier paired with heat_wave_threshold_definition to capture t...
indoor_outdoor Indoor / outdoor regime
input_file_sha256 SHA256 of the input file (CSV / parquet)
input_provenance_id The provenance_id of the upstream sidecar that fully describes this input —...
input_role The standard-name local token of this input's physical quantity (the same qua...
input_row_count Number of rows in the input
input_source_short_code Human-readable short code of the input's source product (e
interval_end End of the interval
interval_start Start of the interval
lag_alignment_applied Whether and how values were lag-aligned to a clinical event
lag_alignment_applied_missing_reason Reason lag_alignment_applied is null
lag_alignment_specifier Free-form specifier paired with lag_alignment_applied to capture the concre...
linkage_buffer_aggregation_method Aggregation method applied within the buffer (mean / max / median / area-weig...
linkage_buffer_aggregation_method_missing_reason Reason linkage_buffer_aggregation_method is null
linkage_buffer_radius_m Buffer radius in metres for buffer-aggregation strategies
linkage_buffer_radius_m_missing_reason Reason linkage_buffer_radius_m is null
linkage_max_distance_to_station_m Maximum distance to a station for nearest-station strategies; values beyond t...
linkage_max_distance_to_station_m_missing_reason Reason linkage_max_distance_to_station_m is null
linkage_method Linkage-method object — see envar_linkage
linkage_strategy How a gridded value is attached to a patient location
linkage_working_crs Coordinate reference system the point-to-cell join was actually executed in, ...
location Spatial metadata specifying where the observation was made - geolocation, pla...
methodology Information about how an observation was made - method, instrument, reagent k...
metric_temporal_aggregation_rule For heat-wave flags, how multi-day exposures are stamped on individual days (...
metric_temporal_aggregation_rule_missing_reason Reason metric_temporal_aggregation_rule is null
missing_data_handling_method How the source handles missing values (e
missing_data_handling_method_missing_reason Reason missing_data_handling_method is null
missing_reason Controlled reason a nullable slot is null
missing_value_sentinel The stored value that means "missing" in the source product's files, verbatim...
model_aggregate_uncertainty Summary statistics for the model as a whole — cross-validation metrics and wh...
model_aggregate_uncertainty_missing_reason Reason model_aggregate_uncertainty is null
native_spatial_resolution_descriptor Human-readable label for the native resolution, e
native_spatial_resolution_m Native spatial resolution of the source product in metres
native_units_ucum UCUM unit of the values as the source product stores them, when that differ...
native_value_column Name of a second column carrying the same values in the source's native uni...
native_value_offset CF-style packing offset applied when decoding the source's stored integers to...
native_value_scale_factor CF-style packing multiplier applied when decoding the source's stored integer...
null_semantics_column Name of a per-value column carrying a null-semantics indicator drawn from `Nu...
null_semantics_column_missing_reason Reason null_semantics_column is null
observation_result The outcome of the observation type - answer, value, result, determination
observation_type Question being asked, measurement being taken, quality being observed
offset Offset from event (e
output_file_sha256 SHA256 of the output file (CSV / parquet)
output_row_count Number of rows in the output
partial_day_attribution_rule How boundary / transition days of the patient's trajectory (trip start / end,...
partial_day_attribution_rule_missing_reason Reason partial_day_attribution_rule is null
per_value_uncertainty_type Kind of per-value uncertainty captured in the column named by `DataLayout
per_value_uncertainty_type_missing_reason Reason per_value_uncertainty_type is null
per_value_uncertainty_units_ucum Units of the per-value uncertainty in UCUM syntax
per_value_uncertainty_units_ucum_missing_reason Reason per_value_uncertainty_units_ucum is null
percentile_reference_geographic_scope Geographic scope over which the reference distribution was computed
percentile_reference_geographic_scope_missing_reason Reason percentile_reference_geographic_scope is null
percentile_reference_period_end End of the reference distribution
percentile_reference_period_end_missing_reason Reason percentile_reference_period_end is null
percentile_reference_period_start Start of the reference distribution used for percentile-based thresholds
percentile_reference_period_start_missing_reason Reason percentile_reference_period_start is null
percentile_reference_seasonal_window Seasonal window over which the reference was computed
percentile_reference_seasonal_window_missing_reason Reason percentile_reference_seasonal_window is null
phi_status Whether the sidecar carries any Protected Health Information
population_weighting_source Census vintage used for population weighting (e
population_weighting_source_missing_reason Reason population_weighting_source is null
privacy_transformation Any privacy-protecting transformation applied to the linked location after ...
privacy_transformation_note Free-text detail of the privacy transformation named in `privacy_transformati...
profile_version Version of microschema profile this conforms to
provenance_chain Ordered W3C-PROV-style chain of upstream tool runs — see envar_toolrun
provenance_chain_steps Ordered list of upstream ToolRuns, from oldest to most recent, whose output...
provenance_chain_terminus_type The kind of root of the chain
provenance_id Stable identifier for this sidecar / record (ULID recommended)
quality_flag_column Name of any per-value QA flag column
quality_flag_column_missing_reason Reason quality_flag_column is null
quality_flag_vocabulary Reference to the QA flag vocabulary (e
quality_flag_vocabulary_missing_reason Reason quality_flag_vocabulary is null
quantity_unit Unit (UCUM, UO, QUDT, etc
quantity_value The numeric value
recommended_citation One-line recommended citation derived from the slots above
record_bookkeeping Sidecar bookkeeping — the schema version the record conforms to, its stable i...
relative_to_event Event this is relative to
reported_in DOI / citation where the aggregate uncertainty is reported
run_arguments The exact argument map passed at invocation, serialised as a JSON string
run_duration_seconds How long the run took, in seconds
run_environment Host OS, Docker / podman version, R / Python version, key library versions, a...
run_log_excerpt Last ~50 lines of the run log, where useful for debugging or audit
run_log_excerpt_missing_reason Reason run_log_excerpt is null
run_timestamp_utc When the run started (UTC)
schema_version The version of the EnVar micro-schema this document conforms to
solar_radiation_basis For WBGT / UTCI inputs, the basis used for solar radiation
solar_radiation_basis_missing_reason Reason solar_radiation_basis is null
source_access_url Landing-page URL for the dataset (not a download link, which rots)
source_acdd_attributes Passthrough of ACDD (Attribute Convention for Data Discovery) global attribut...
source_acdd_attributes_missing_reason Reason source_acdd_attributes is null
source_citation_apa Full APA-style citation for the source dataset
source_citation_bibtex BibTeX entry for the source dataset, machine-parseable
source_citation_bibtex_missing_reason Reason source_citation_bibtex is null
source_dataset Source dataset object — see envar_source
source_dataset_doi DOI of the source dataset
source_dataset_doi_missing_reason Reason source_dataset_doi is null
source_dataset_name Full name of the source product, e
source_dataset_short_code Short code keying into the EnVar source registry, e
source_dataset_spatial_extent Human-readable spatial extent of the product, e
source_dataset_temporal_coverage Source product temporal coverage as an ISO 8601 interval string `/<end...
source_dataset_version Source product version
source_homogenisation_status For station-based products, whether values have been homogenised
source_homogenisation_status_missing_reason Reason source_homogenisation_status is null
source_license_spdx SPDX identifier of the source license, e
source_native_format Format the source ships in
source_producer_institution Producer institution, e
spatial_aggregation_preserves What quantity the spatial-aggregation operator is meant to preserve when a ...
spatial_extent_bbox Bounding box of the source product (not the extracted subset), as `[min_lon...
spatial_extent_descriptor Human-readable description of the product extent, e
spatial_reference Spatial reference object describing the native grid and extraction
standard_name The standard-name identifier for the physical quantity, as a CURIE so the sch...
subject Entity being measured, observed, or interviewed - person, animal, specimen, o...
subject_age Age of the subject at this timepoint (e
subject_column Name of the column carrying the opaque subject / cohort identifier the record...
table_orientation Whether the companion file is wide (one column per variable) or long (one `va...
target_concept_id Concept identifier for the variable in the vocabulary named by `target_concep...
target_concept_id_missing_reason Reason target_concept_id is null
target_concept_vocabulary The downstream health-data vocabulary that target_concept_id and `concept_s...
target_geography_type Geographic unit the exposure value is attached to
temporal_aggregation_method How the value summarises sub-period values
temporal_aggregation_window_seconds Redundant with temporal_resolution but explicit for machine use; e
temporal_coverage_end End of the source product's coverage
temporal_coverage_start Start of the source product's full temporal coverage
temporal_reference Temporal reference object describing resolution, aggregation, and day-boundar...
temporal_resolution Native temporal grain of the values
temporality Temporal metadata specifying when an observation was made
time_column Name of the column carrying the observation date / timestamp (e
tool_description One-line tool description (from the tool's dht env var or equivalent)
tool_name Tool name, e
tool_run The current ToolRun — see envar_toolrun
tool_version Semver tool version
uncertainty Uncertainty object — see envar_uncertainty
unit_conversion_formula The conversion from the source's native representation to the values in the c...
units_display Human-readable unit string for display purposes, e
units_ucum The unit expressed in UCUM syntax, e
value_column Name of the column carrying this record's exposure values, e
value_data_type The data type of the stored exposure value
value_range_plausible_max Physical / domain upper bound for plausible values (e
value_range_plausible_min Physical / domain lower bound for plausible values (e
value_uncertainty_column Name of the column carrying per-value uncertainty (e
value_uncertainty_column_missing_reason Reason value_uncertainty_column is null
variable_column For long orientation: name of the column that discriminates variables (e
variable_identity The variable identity object — what physical quantity is being captured
variable_key For long orientation: the value in variable_column that selects this record...
variable_label Human-readable label, e
variable_name Short machine-readable name for the variable, usually the name the upstream t...
variable_specific_extensions Methodology blocks that only apply to particular variable families — present ...
wind_speed_measurement_height_m For WBGT and UTCI inputs, the wind-speed measurement height in metres
wind_speed_measurement_height_m_missing_reason Reason wind_speed_measurement_height_m is null