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Patch 547 #566

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Dec 21, 2024
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158 changes: 154 additions & 4 deletions NF.jsonld
Original file line number Diff line number Diff line change
Expand Up @@ -18027,6 +18027,105 @@
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:EpidemiologyMetric",
"@type": "rdfs:Class",
"rdfs:comment": "Common metrics used in epidemiology studies.",
"rdfs:label": "EpidemiologyMetric",
"rdfs:subClassOf": [
{
"@id": "bts:Thing"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"schema:rangeIncludes": [
{
"@id": "bts:StandardizedIncidenceRatio"
},
{
"@id": "bts:IncidenceRate"
},
{
"@id": "bts:MortalityRate"
},
{
"@id": "bts:StandardizedMortalityRatio"
}
],
"sms:displayName": "epidemiologyMetric",
"sms:required": "sms:true",
"sms:validationRules": []
},
{
"@id": "bts:StandardizedIncidenceRatio",
"@type": "rdfs:Class",
"rdfs:comment": "TBD",
"rdfs:label": "StandardizedIncidenceRatio",
"rdfs:subClassOf": [
{
"@id": "bts:EpidemiologyMetric"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "Standardized Incidence Ratio",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:IncidenceRate",
"@type": "rdfs:Class",
"rdfs:comment": "TBD",
"rdfs:label": "IncidenceRate",
"rdfs:subClassOf": [
{
"@id": "bts:EpidemiologyMetric"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "Incidence Rate",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:MortalityRate",
"@type": "rdfs:Class",
"rdfs:comment": "TBD",
"rdfs:label": "MortalityRate",
"rdfs:subClassOf": [
{
"@id": "bts:EpidemiologyMetric"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "Mortality Rate",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:StandardizedMortalityRatio",
"@type": "rdfs:Class",
"rdfs:comment": "TBD",
"rdfs:label": "StandardizedMortalityRatio",
"rdfs:subClassOf": [
{
"@id": "bts:EpidemiologyMetric"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "Standardized Mortality Ratio",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:SampleType",
"@type": "rdfs:Class",
Expand Down Expand Up @@ -19548,7 +19647,7 @@
"@id": "bts:DataIndex"
},
{
"@id": "bts:StandardizedIncidenceRatio"
"@id": "bts:AggregatedData"
},
{
"@id": "bts:DescriptiveMetadata"
Expand Down Expand Up @@ -20200,10 +20299,10 @@
"sms:validationRules": []
},
{
"@id": "bts:StandardizedIncidenceRatio",
"@id": "bts:AggregatedData",
"@type": "rdfs:Class",
"rdfs:comment": "TBD",
"rdfs:label": "StandardizedIncidenceRatio",
"rdfs:label": "AggregatedData",
"rdfs:subClassOf": [
{
"@id": "bts:DataType"
Expand All @@ -20212,7 +20311,7 @@
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "StandardizedIncidenceRatio",
"sms:displayName": "AggregatedData",
"sms:required": "sms:false",
"sms:validationRules": []
},
Expand Down Expand Up @@ -26858,6 +26957,23 @@
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:PopulationCoverage",
"@type": "rdfs:Class",
"rdfs:comment": "Describes population coverage of the present data.",
"rdfs:label": "PopulationCoverage",
"rdfs:subClassOf": [
{
"@id": "bts:Thing"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "populationCoverage",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:IndividualID",
"@type": "rdfs:Class",
Expand Down Expand Up @@ -37824,6 +37940,40 @@
],
"sms:validationRules": []
},
{
"@id": "bts:EpidemiologyDataTemplate",
"@type": "rdfs:Class",
"rdfs:comment": "For aggregated data from defined populations or cohorts, used in/derived from epidemiology studies.",
"rdfs:label": "EpidemiologyDataTemplate",
"rdfs:subClassOf": [
{
"@id": "bts:Template"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "EpidemiologyDataTemplate",
"sms:required": "sms:false",
"sms:requiresDependency": [
{
"@id": "bts:ResourceType"
},
{
"@id": "bts:DataType"
},
{
"@id": "bts:FileFormat"
},
{
"@id": "bts:PopulationCoverage"
},
{
"@id": "bts:EpidemiologyMetric"
}
],
"sms:validationRules": []
},
{
"@id": "bts:HumanCohortTemplate",
"@type": "rdfs:Class",
Expand Down
7 changes: 3 additions & 4 deletions modules/Data/Data.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -112,10 +112,9 @@ enums:
dataIndex:
description: A data index is information used to help with retrieval of some other data, especially large-scale data that would benefit from such an index. Very common formats are .bai and .tbi.
meaning: http://edamontology.org/data_0955
StandardizedIncidenceRatio:
description: The standardized incidence ratio (SIR) is often used to assess whether there is an excess number of cancer cases, considering what is “expected” to occur within an area over time given existing knowledge of the type of cancer and the local population at risk.
source: https://www.cdc.gov/cancer-environment/php/guidelines/statistical-considerations.html

AggregatedData:
description: Summary or group-level data.

DataSubtypeEnum:
permissible_values:
normalized:
Expand Down
13 changes: 11 additions & 2 deletions modules/Template/Data.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -788,7 +788,6 @@ classes:
close_mappings:
- https://www.immport.org/shared/dataModelDocumentation?table=fcs_analyzed_result


MaterialScienceAssayTemplate:
is_a: NonBiologicalAssayDataTemplate
description: General template for describing data for a materials science assay.
Expand Down Expand Up @@ -852,7 +851,17 @@ classes:
#######################################
# Other Data Artifacts
#######################################


EpidemiologyDataTemplate:
is_a: Template
description: For aggregated data from defined populations or cohorts, used in/derived from epidemiology studies.
slots:
- resourceType
- dataType
- fileFormat
- populationCoverage
- epidemiologyMetric

WorkflowReport:
is_a: Template
description: Template used for miscellaneous workflow reports and accessory files
Expand Down
11 changes: 11 additions & 0 deletions modules/props.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -386,6 +386,14 @@ slots:
description: String describing general class of drug screen
range: DrugScreen
required: false
epidemiologyMetric:
description: Common metrics used in epidemiology studies.
required: true
enum_range:
- Standardized Incidence Ratio
- Incidence Rate
- Mortality Rate
- Standardized Mortality Ratio
etag:
description: Synapse employs an Optimistic Concurrency Control (OCC) scheme to
handle concurrent updates. The E-Tag changes every time an entity is
Expand Down Expand Up @@ -799,6 +807,9 @@ slots:
range: PlexiformNeurofibromaManifestationEnum
required: false
title: Plexiform neurofibromas
populationCoverage:
description: Describes population coverage of the present data.
required: false
programmingLanguage:
description: A computer programming language
enum_range:
Expand Down
2 changes: 1 addition & 1 deletion registered-json-schemas/PortalDataset.json
Original file line number Diff line number Diff line change
Expand Up @@ -259,7 +259,7 @@
"electrophysiology",
"audio transcript",
"dataIndex",
"StandardizedIncidenceRatio"
"AggregatedData"
],
"title": "Data",
"type": "string"
Expand Down
2 changes: 1 addition & 1 deletion registered-json-schemas/PortalStudy.json
Original file line number Diff line number Diff line change
Expand Up @@ -62,7 +62,7 @@
"electrophysiology",
"audio transcript",
"dataIndex",
"StandardizedIncidenceRatio"
"AggregatedData"
],
"title": "Data",
"type": "string"
Expand Down
2 changes: 1 addition & 1 deletion registered-json-schemas/Superdataset.json
Original file line number Diff line number Diff line change
Expand Up @@ -259,7 +259,7 @@
"electrophysiology",
"audio transcript",
"dataIndex",
"StandardizedIncidenceRatio"
"AggregatedData"
],
"title": "Data",
"type": "string"
Expand Down
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