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DataDog/dd-sdk-reactnative | 2b259f57deeb535b33164aff0df41ecbd9321570 | 2024-03-22T15:51:36 | packages/core/datadog-configuration.schema.json | 108 | 2024-05-28T05:03:43.083856Z | {
"$id": "https://github.com/DataDog/dd-sdk-reactnative/blob/develop/datadog-configuration.schema.json",
"$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "Configuration for initializing the Datadog React Native SDK from the native layers.",
"properties": {
"configuration": {
"description": "Configuration used for initializing the Datadog SDK.",
"properties": {
"actionNameAttribute": {
"description": "Specifies a custom prop to name RUM actions on elements having an `onPress` prop.",
"type": "string"
},
"applicationId": {
"description": "The RUM application ID.",
"type": "string"
},
"batchSize": {
"description": "Defines the Datadog SDK policy when batching data together before uploading it to Datadog servers.",
"enum": [
"SMALL",
"MEDIUM",
"LARGE"
],
"type": "string"
},
"bundleLogsWithRum": {
"description": "Enables RUM correlation with logs.",
"type": "boolean"
},
"bundleLogsWithTraces": {
"description": "Enables Traces correlation with logs.",
"type": "boolean"
},
"clientToken": {
"description": "A valid Datadog client token.",
"type": "string"
},
"customEndpoints": {
"description": "Target a custom server for RUM, Logs and Traces features.",
"properties": {
"logs": {
"type": "string"
},
"rum": {
"type": "string"
},
"trace": {
"type": "string"
}
},
"type": "object"
},
"env": {
"description": "The application\u2019s environment, for example: prod, pre-prod, staging, etc.",
"type": "string"
},
"firstPartyHosts": {
"description": "List of your backends hosts to enable tracing with.",
"items": {
"properties": {
"match": {
"description": "Matches domains and subdomains, e.g. `['example.com']` matches `example.com` and `api.example.com`. Regular expressions are NOT supported.",
"type": "string"
},
"propagatorTypes": {
"description": "Types of instrumentation on the host.",
"items": {
"description": "Type of instrumentation on the host.",
"enum": [
"DATADOG",
"B3",
"B3MULTI",
"TRACECONTEXT"
],
"type": "string"
},
"type": "array"
}
},
"type": "object"
},
"type": "array"
},
"longTaskThresholdMs": {
"description": "The threshold for javascript long tasks reporting in milliseconds.",
"type": "integer"
},
"nativeCrashReportEnabled": {
"description": "Enables crash reporting for native platforms (iOS, Android). Default `false`.",
"type": "boolean"
},
"nativeInteractionTracking": {
"description": "Enables native interaction tracking.",
"type": "boolean"
},
"nativeLongTaskThresholdMs": {
"description": "The threshold for native long tasks reporting in milliseconds.",
"type": "integer"
},
"nativeViewTracking": {
"description": "Enables native views tracking.",
"type": "boolean"
},
"proxy": {
"description": "Configuration for proxying SDK data.",
"properties": {
"address": {
"description": "Proxy address. Can be either in the IP address format, ex. '1.1.1.1', or hostname, ex. 'example.com'.",
"type": "string"
},
"password": {
"description": "Password for Basic authentication scheme.",
"type": "string"
},
"port": {
"description": "Proxy port.",
"type": "integer"
},
"type": {
"description": "Proxy type.",
"enum": [
"HTTP",
"HTTPS",
"SOCKS"
],
"type": "string"
},
"username": {
"description": "Username for Basic authentication scheme. Note: SOCKS + authentication scheme is not supported.",
"type": "string"
}
},
"required": [
"type",
"port",
"address"
],
"type": "object"
},
"resourceTracingSamplingRate": {
"description": "Percentage of tracing integrations for network calls between your app and your backend. Range `0`-`100`.",
"type": "number"
},
"serviceName": {
"description": "Custom service name.",
"type": "string"
},
"sessionSamplingRate": {
"description": "Percentage of sampled RUM sessions. Range `0`-`100`.",
"type": "integer"
},
"site": {
"description": "The Datadog site of your organization (can be 'US1', 'US1_FED', 'US3', 'US5', 'AP1' or 'EU1', default is 'US1').",
"enum": [
"US1",
"US1_FED",
"US3",
"US5",
"EU1",
"AP1"
],
"type": "string"
},
"telemetrySampleRate": {
"description": "The sampling rate for Internal Telemetry (info related to the work of the SDK internals). Range `0`-`100`.",
"type": "integer"
},
"trackBackgroundEvents": {
"description": "Enables tracking of RUM event when no RUM View is active.",
"type": "boolean"
},
"trackErrors": {
"description": "Track React Native errors.",
"type": "boolean"
},
"trackFrustrations": {
"description": "Enables tracking of frustration signals (error taps). Defaults to `true`.",
"type": "boolean"
},
"trackInteractions": {
"description": "Track React Native components interactions.",
"type": "boolean"
},
"trackResources": {
"description": "Track React Native resources.",
"type": "boolean"
},
"trackingConsent": {
"description": "Consent, which can take one of the following values: 'PENDING', 'GRANTED', 'NOT_GRANTED'.",
"enum": [
"PENDING",
"GRANTED",
"NOT_GRANTED"
],
"type": "string"
},
"uploadFrequency": {
"description": "Sets the preferred frequency for uploading batches of data.",
"enum": [
"RARE",
"AVERAGE",
"FREQUENT"
],
"type": "string"
},
"verbosity": {
"description": "Verbosity for internal SDK logging.",
"enum": [
"DEBUG",
"INFO",
"WARN",
"ERROR"
],
"type": "string"
},
"version": {
"description": "Overrides the reported version of the app.",
"type": "string"
},
"vitalsUpdateFrequency": {
"description": "Sets the preferred frequency for collecting mobile vitals.",
"enum": [
"NEVER",
"RARE",
"AVERAGE",
"FREQUENT"
],
"type": "string"
}
},
"required": [
"clientToken",
"env",
"applicationId"
],
"type": "object"
}
},
"title": "Datadog React Native SDK Configuration",
"type": "object"
} | Apache-2.0 | en |
DataDog/dd-sdk-reactnative | c6cd92f993877c97b9d3eaaf11a2f79dd6fb76e8 | 2024-03-22T13:20:52 | packages/core/datadog-configuration.schema.json | 108 | 2024-05-28T05:03:43.083856Z | {
"$id": "https://github.com/DataDog/dd-sdk-reactnative/blob/develop/datadog-configuration.schema.json",
"$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "Configuration for initializing the Datadog React Native SDK from the native layers.",
"properties": {
"configuration": {
"description": "Configuration used for initializing the Datadog SDK.",
"properties": {
"applicationId": {
"description": "The RUM application ID.",
"type": "string"
},
"batchSize": {
"description": "Defines the Datadog SDK policy when batching data together before uploading it to Datadog servers.",
"enum": [
"SMALL",
"MEDIUM",
"LARGE"
],
"type": "string"
},
"clientToken": {
"description": "A valid Datadog client token.",
"type": "string"
},
"customEndpoints": {
"description": "Target a custom server for RUM, Logs and Traces features.",
"properties": {
"logs": {
"type": "string"
},
"rum": {
"type": "string"
},
"trace": {
"type": "string"
}
},
"type": "object"
},
"env": {
"description": "The application\u2019s environment, for example: prod, pre-prod, staging, etc.",
"type": "string"
},
"firstPartyHosts": {
"description": "List of your backends hosts to enable tracing with.",
"items": {
"properties": {
"match": {
"description": "Matches domains and subdomains, e.g. `['example.com']` matches `example.com` and `api.example.com`. Regular expressions are NOT supported.",
"type": "string"
},
"propagatorTypes": {
"description": "Types of instrumentation on the host.",
"items": {
"description": "Type of instrumentation on the host.",
"enum": [
"DATADOG",
"B3",
"B3MULTI",
"TRACECONTEXT"
],
"type": "string"
},
"type": "array"
}
},
"type": "object"
},
"type": "array"
},
"longTaskThresholdMs": {
"description": "The threshold for javascript long tasks reporting in milliseconds.",
"type": "integer"
},
"nativeCrashReportEnabled": {
"description": "Enables crash reporting for native platforms (iOS, Android). Default `false`.",
"type": "boolean"
},
"nativeInteractionTracking": {
"description": "Enables native interaction tracking.",
"type": "boolean"
},
"nativeLongTaskThresholdMs": {
"description": "The threshold for native long tasks reporting in milliseconds.",
"type": "integer"
},
"nativeViewTracking": {
"description": "Enables native views tracking.",
"type": "boolean"
},
"proxy": {
"description": "Configuration for proxying SDK data.",
"properties": {
"address": {
"description": "Proxy address. Can be either in the IP address format, ex. '1.1.1.1', or hostname, ex. 'example.com'.",
"type": "string"
},
"password": {
"description": "Password for Basic authentication scheme.",
"type": "string"
},
"port": {
"description": "Proxy port.",
"type": "integer"
},
"type": {
"description": "Proxy type.",
"enum": [
"HTTP",
"HTTPS",
"SOCKS"
],
"type": "string"
},
"username": {
"description": "Username for Basic authentication scheme. Note: SOCKS + authentication scheme is not supported.",
"type": "string"
}
},
"required": [
"type",
"port",
"address"
],
"type": "object"
},
"serviceName": {
"description": "Custom service name.",
"type": "string"
},
"sessionSamplingRate": {
"description": "Percentage of sampled RUM sessions. Range `0`-`100`.",
"type": "integer"
},
"site": {
"description": "The Datadog site of your organization (can be 'US1', 'US1_FED', 'US3', 'US5', 'AP1' or 'EU1', default is 'US1').",
"enum": [
"US1",
"US1_FED",
"US3",
"US5",
"EU1",
"AP1"
],
"type": "string"
},
"telemetrySampleRate": {
"description": "The sampling rate for Internal Telemetry (info related to the work of the SDK internals). Range `0`-`100`.",
"type": "integer"
},
"trackBackgroundEvents": {
"description": "Enables tracking of RUM event when no RUM View is active.",
"type": "boolean"
},
"trackFrustrations": {
"description": "Enables tracking of frustration signals (error taps). Defaults to `true`.",
"type": "boolean"
},
"trackingConsent": {
"description": "Consent, which can take one of the following values: 'PENDING', 'GRANTED', 'NOT_GRANTED'.",
"enum": [
"PENDING",
"GRANTED",
"NOT_GRANTED"
],
"type": "string"
},
"uploadFrequency": {
"description": "Sets the preferred frequency for uploading batches of data.",
"enum": [
"RARE",
"AVERAGE",
"FREQUENT"
],
"type": "string"
},
"verbosity": {
"description": "Verbosity for internal SDK logging.",
"enum": [
"DEBUG",
"INFO",
"WARN",
"ERROR"
],
"type": "string"
},
"version": {
"description": "Overrides the reported version of the app.",
"type": "string"
},
"vitalsUpdateFrequency": {
"description": "Sets the preferred frequency for collecting mobile vitals.",
"enum": [
"NEVER",
"RARE",
"AVERAGE",
"FREQUENT"
],
"type": "string"
}
},
"required": [
"clientToken",
"env",
"applicationId"
],
"type": "object"
}
},
"title": "Datadog React Native SDK Configuration",
"type": "object"
} | Apache-2.0 | en |
DataDog/dd-sdk-reactnative | 2a3762650541da500eb7951d195cebc32f606597 | 2024-03-22T13:20:52 | packages/core/datadog-configuration.schema.json | 108 | 2024-05-28T05:03:43.083856Z | {
"$id": "https://github.com/DataDog/dd-sdk-reactnative/blob/develop/datadog-configuration.schema.json",
"$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "Configuration for initializing the Datadog React Native SDK from the native layers.",
"properties": {
"configuration": {
"description": "Configuration used for initializing the Datadog SDK.",
"properties": {
"actionNameAttribute": {
"description": "Specifies a custom prop to name RUM actions on elements having an `onPress` prop.",
"type": "string"
},
"applicationId": {
"description": "The RUM application ID.",
"type": "string"
},
"batchSize": {
"description": "Defines the Datadog SDK policy when batching data together before uploading it to Datadog servers.",
"enum": [
"SMALL",
"MEDIUM",
"LARGE"
],
"type": "string"
},
"clientToken": {
"description": "A valid Datadog client token.",
"type": "string"
},
"customEndpoints": {
"description": "Target a custom server for RUM, Logs and Traces features.",
"properties": {
"logs": {
"type": "string"
},
"rum": {
"type": "string"
},
"trace": {
"type": "string"
}
},
"type": "object"
},
"env": {
"description": "The application\u2019s environment, for example: prod, pre-prod, staging, etc.",
"type": "string"
},
"firstPartyHosts": {
"description": "List of your backends hosts to enable tracing with.",
"items": {
"properties": {
"match": {
"description": "Matches domains and subdomains, e.g. `['example.com']` matches `example.com` and `api.example.com`. Regular expressions are NOT supported.",
"type": "string"
},
"propagatorTypes": {
"description": "Types of instrumentation on the host.",
"items": {
"description": "Type of instrumentation on the host.",
"enum": [
"DATADOG",
"B3",
"B3MULTI",
"TRACECONTEXT"
],
"type": "string"
},
"type": "array"
}
},
"type": "object"
},
"type": "array"
},
"longTaskThresholdMs": {
"description": "The threshold for javascript long tasks reporting in milliseconds.",
"type": "integer"
},
"nativeCrashReportEnabled": {
"description": "Enables crash reporting for native platforms (iOS, Android). Default `false`.",
"type": "boolean"
},
"nativeInteractionTracking": {
"description": "Enables native interaction tracking.",
"type": "boolean"
},
"nativeLongTaskThresholdMs": {
"description": "The threshold for native long tasks reporting in milliseconds.",
"type": "integer"
},
"nativeViewTracking": {
"description": "Enables native views tracking.",
"type": "boolean"
},
"proxy": {
"description": "Configuration for proxying SDK data.",
"properties": {
"address": {
"description": "Proxy address. Can be either in the IP address format, ex. '1.1.1.1', or hostname, ex. 'example.com'.",
"type": "string"
},
"password": {
"description": "Password for Basic authentication scheme.",
"type": "string"
},
"port": {
"description": "Proxy port.",
"type": "integer"
},
"type": {
"description": "Proxy type.",
"enum": [
"HTTP",
"HTTPS",
"SOCKS"
],
"type": "string"
},
"username": {
"description": "Username for Basic authentication scheme. Note: SOCKS + authentication scheme is not supported.",
"type": "string"
}
},
"required": [
"type",
"port",
"address"
],
"type": "object"
},
"resourceTracingSamplingRate": {
"description": "Percentage of tracing integrations for network calls between your app and your backend. Range `0`-`100`.",
"type": "number"
},
"serviceName": {
"description": "Custom service name.",
"type": "string"
},
"sessionSamplingRate": {
"description": "Percentage of sampled RUM sessions. Range `0`-`100`.",
"type": "integer"
},
"site": {
"description": "The Datadog site of your organization (can be 'US1', 'US1_FED', 'US3', 'US5', 'AP1' or 'EU1', default is 'US1').",
"enum": [
"US1",
"US1_FED",
"US3",
"US5",
"EU1",
"AP1"
],
"type": "string"
},
"telemetrySampleRate": {
"description": "The sampling rate for Internal Telemetry (info related to the work of the SDK internals). Range `0`-`100`.",
"type": "integer"
},
"trackBackgroundEvents": {
"description": "Enables tracking of RUM event when no RUM View is active.",
"type": "boolean"
},
"trackErrors": {
"description": "Track React Native errors.",
"type": "boolean"
},
"trackFrustrations": {
"description": "Enables tracking of frustration signals (error taps). Defaults to `true`.",
"type": "boolean"
},
"trackInteractions": {
"description": "Track React Native components interactions.",
"type": "boolean"
},
"trackResources": {
"description": "Track React Native resources.",
"type": "boolean"
},
"trackingConsent": {
"description": "Consent, which can take one of the following values: 'PENDING', 'GRANTED', 'NOT_GRANTED'.",
"enum": [
"PENDING",
"GRANTED",
"NOT_GRANTED"
],
"type": "string"
},
"uploadFrequency": {
"description": "Sets the preferred frequency for uploading batches of data.",
"enum": [
"RARE",
"AVERAGE",
"FREQUENT"
],
"type": "string"
},
"verbosity": {
"description": "Verbosity for internal SDK logging.",
"enum": [
"DEBUG",
"INFO",
"WARN",
"ERROR"
],
"type": "string"
},
"version": {
"description": "Overrides the reported version of the app.",
"type": "string"
},
"vitalsUpdateFrequency": {
"description": "Sets the preferred frequency for collecting mobile vitals.",
"enum": [
"NEVER",
"RARE",
"AVERAGE",
"FREQUENT"
],
"type": "string"
}
},
"required": [
"clientToken",
"env",
"applicationId"
],
"type": "object"
}
},
"title": "Datadog React Native SDK Configuration",
"type": "object"
} | Apache-2.0 | en |
redhat-certification/chart-verifier | 2f4896f9134521aaee442f9de0cf38c47376a7be | 2022-07-18T19:59:16 | internal/chartverifier/checks/chart/values.schema.json | 51 | 2024-05-28T01:04:48.786071Z | {
"$schema": "https://json-schema.org/draft-07/schema#",
"properties": {
"image": {
"description": "Container Image",
"properties": {
"repo": {
"type": "string"
},
"tag": {
"type": "string"
}
},
"type": "object"
},
"name": {
"description": "Service name",
"type": "string"
},
"port": {
"description": "Port",
"minimum": 0,
"type": "integer"
},
"protocol": {
"type": "string"
}
},
"required": [
"protocol",
"port"
],
"title": "Values",
"type": "object"
} | Apache-2.0 | en |
AMRC-FactoryPlus/amrc-connectivity-stack | 4a5a65fd6e3700ea7fc1c19153a1e21686536f3e | 2024-03-22T10:30:34 | acs-configdb/config-schema/General_Information.json | 10 | 2024-05-27T03:11:06.82779Z | {
"$id": "urn:uuid:64a8bfa9-7772-45c4-9d1a-9e6290690957",
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false,
"description": "Human-readble information for display in UIs and such.",
"properties": {
"contact": {
"description": "Contact information for the people responsible for this object.",
"items": {
"properties": {
"email": {
"format": "email",
"type": "string"
},
"name": {
"type": "string"
}
},
"required": [
"name"
],
"type": "object"
},
"type": "array"
},
"location": {
"description": "A brief human-readable description of the object's physical location.",
"type": "string"
},
"name": {
"description": "A human-readable name for this object.",
"type": "string"
},
"photo": {
"description": "A photo of the object to display in selection screens and so on.",
"format": "byte",
"type": "string"
}
},
"required": [
"name"
],
"title": "Device general information",
"type": "object"
} | MIT | en |
huntandhackett/Antignis | 778216802f4dab0ad7de93c484cc056369a83cd2 | 2022-10-21T08:47:51 | Misc/JSONSchema.json | 36 | 2024-05-27T06:43:47.532802Z | {
"$id": "http://example.com/example.json",
"$schema": "https://json-schema.org/draft/2019-09/schema",
"default": {},
"properties": {
"DNSHostname": {
"default": "",
"examples": [
"VM01.rebel.local"
],
"title": "The DNSHostname Schema",
"type": "string"
},
"FileShare": {
"default": [],
"examples": [
[
{
"Host": null,
"HostId": 0,
"Id": 0,
"Name": "tmp"
}
]
],
"items": {
"examples": [
{
"Host": null,
"HostId": 0,
"Id": 0,
"Name": "tmp"
}
],
"properties": {
"Host": {
"examples": [
null
],
"title": "The Host Schema",
"type": "null"
},
"HostId": {
"examples": [
0
],
"title": "The HostId Schema",
"type": "integer"
},
"Id": {
"examples": [
0
],
"title": "The Id Schema",
"type": "integer"
},
"Name": {
"examples": [
"Conf",
"tmp"
],
"title": "The Name Schema",
"type": "string"
}
},
"required": [
"HostId",
"Id",
"Host",
"Name"
],
"title": "A Schema",
"type": "object"
},
"title": "The FileShare Schema",
"type": "array"
},
"IPAddress": {
"default": "",
"examples": [
"192.168.88.128"
],
"title": "The IPAddress Schema",
"type": "string"
},
"Id": {
"default": 0,
"examples": [
0
],
"title": "The Id Schema",
"type": "integer"
},
"IsServerOS": {
"default": false,
"examples": [
false
],
"title": "The IsServerOS Schema",
"type": "boolean"
},
"NetworkMask": {
"default": "",
"examples": [
"255.255.255.0"
],
"title": "The NetworkMask Schema",
"type": "string"
},
"OperatingSystem": {
"default": "",
"examples": [
"Windows 10 Enterprise"
],
"title": "The OperatingSystem Schema",
"type": "string"
},
"Port": {
"default": [],
"examples": [
[
{
"Host": null,
"HostId": 0,
"Id": 0,
"PortNumber": 135
},
{
"Host": null,
"HostId": 0,
"Id": 0,
"PortNumber": 445
},
{
"Host": null,
"HostId": 0,
"Id": 0,
"PortNumber": 139
}
]
],
"items": {
"examples": [
{
"Host": null,
"HostId": 0,
"Id": 0,
"PortNumber": 135
},
{
"Host": null,
"HostId": 0,
"Id": 0,
"PortNumber": 445
},
{
"Host": null,
"HostId": 0,
"Id": 0,
"PortNumber": 139
}
],
"properties": {
"Host": {
"examples": [
null
],
"title": "The Host Schema",
"type": "null"
},
"HostId": {
"examples": [
0
],
"title": "The HostId Schema",
"type": "integer"
},
"Id": {
"examples": [
0
],
"title": "The Id Schema",
"type": "integer"
},
"PortNumber": {
"examples": [
135,
445,
139
],
"title": "The PortNumber Schema",
"type": "integer"
}
},
"required": [
"PortNumber",
"HostId",
"Id",
"Host"
],
"title": "A Schema",
"type": "object"
},
"title": "The Port Schema",
"type": "array"
},
"Program": {
"default": [],
"examples": [
[
{
"Host": null,
"HostId": 0,
"Id": 0,
"Name": "Microsoft Edge"
}
]
],
"items": {
"properties": {
"Host": {
"examples": [
null
],
"title": "The Host Schema",
"type": "null"
},
"HostId": {
"examples": [
0
],
"title": "The HostId Schema",
"type": "integer"
},
"Id": {
"examples": [
0
],
"title": "The Id Schema",
"type": "integer"
},
"Name": {
"examples": [
"Microsoft Edge"
],
"title": "The Name Schema",
"type": "string"
}
},
"required": [
"HostId",
"Id",
"Host",
"Name"
],
"title": "A Schema",
"type": "object"
},
"title": "The Program Schema",
"type": "array"
},
"Role": {
"default": null,
"examples": [
null
],
"title": "The Role Schema",
"type": "null"
},
"TCPConnection": {
"default": [],
"examples": [
[
{
"Direction": "Outbound",
"Host": null,
"HostId": 0,
"Id": 0,
"LocalIPAddress": "192.168.88.128",
"LocalPort": 51509,
"RemoteIPAddress": "192.168.88.132",
"RemotePort": 445
},
{
"Direction": "Outbound",
"Host": null,
"HostId": 0,
"Id": 0,
"LocalIPAddress": "192.168.88.128",
"LocalPort": 51513,
"RemoteIPAddress": "192.168.88.132",
"RemotePort": 445
},
{
"Direction": "Outbound",
"Host": null,
"HostId": 0,
"Id": 0,
"LocalIPAddress": "192.168.88.128",
"LocalPort": 51667,
"RemoteIPAddress": "192.168.88.132",
"RemotePort": 445
},
{
"Direction": "Outbound",
"Host": null,
"HostId": 0,
"Id": 0,
"LocalIPAddress": "192.168.88.128",
"LocalPort": 51708,
"RemoteIPAddress": "192.168.88.132",
"RemotePort": 445
}
]
],
"items": {
"examples": [
{
"Direction": "Outbound",
"Host": null,
"HostId": 0,
"Id": 0,
"LocalIPAddress": "192.168.88.128",
"LocalPort": 51509,
"RemoteIPAddress": "192.168.88.132",
"RemotePort": 445
},
{
"Direction": "Outbound",
"Host": null,
"HostId": 0,
"Id": 0,
"LocalIPAddress": "192.168.88.128",
"LocalPort": 51513,
"RemoteIPAddress": "192.168.88.132",
"RemotePort": 445
},
{
"Direction": "Outbound",
"Host": null,
"HostId": 0,
"Id": 0,
"LocalIPAddress": "192.168.88.128",
"LocalPort": 51667,
"RemoteIPAddress": "192.168.88.132",
"RemotePort": 445
},
{
"Direction": "Outbound",
"Host": null,
"HostId": 0,
"Id": 0,
"LocalIPAddress": "192.168.88.128",
"LocalPort": 51708,
"RemoteIPAddress": "192.168.88.132",
"RemotePort": 445
}
],
"properties": {
"Direction": {
"examples": [
"Outbound"
],
"title": "The Direction Schema",
"type": "string"
},
"Host": {
"examples": [
null
],
"title": "The Host Schema",
"type": "null"
},
"HostId": {
"examples": [
0
],
"title": "The HostId Schema",
"type": "integer"
},
"Id": {
"examples": [
0
],
"title": "The Id Schema",
"type": "integer"
},
"LocalIPAddress": {
"examples": [
"192.168.88.128"
],
"title": "The LocalIPAddress Schema",
"type": "string"
},
"LocalPort": {
"examples": [
51509,
51513,
51667,
51708
],
"title": "The LocalPort Schema",
"type": "integer"
},
"RemoteIPAddress": {
"examples": [
"192.168.88.132"
],
"title": "The RemoteIPAddress Schema",
"type": "string"
},
"RemotePort": {
"examples": [
445
],
"title": "The RemotePort Schema",
"type": "integer"
}
},
"required": [
"RemotePort",
"LocalPort",
"HostId",
"Id",
"Host",
"RemoteIPAddress",
"LocalIPAddress",
"Direction"
],
"title": "A Schema",
"type": "object"
},
"title": "The TCPConnection Schema",
"type": "array"
},
"WindowsFirewallRule": {
"default": [],
"examples": [
[
{
"Action": "NET_FW_ACTION_ALLOW",
"Host": null,
"HostId": 0,
"Id": 0,
"Interfaces": null,
"LocalPorts": "445",
"Name": "DFS Management (SMB-In)",
"Profiles": "NET_FW_PROFILE2_ALL",
"RemoteAddresses": "*",
"RuleEnabled": true
},
{
"Action": "NET_FW_ACTION_ALLOW",
"Host": null,
"HostId": 0,
"Id": 0,
"Interfaces": null,
"LocalPorts": "139",
"Name": "File and Printer Sharing (NB-Session-In)",
"Profiles": "NET_FW_PROFILE2_DOMAIN",
"RemoteAddresses": "*",
"RuleEnabled": true
}
]
],
"items": {
"examples": [
{
"Action": "NET_FW_ACTION_ALLOW",
"Host": null,
"HostId": 0,
"Id": 0,
"Interfaces": null,
"LocalPorts": "445",
"Name": "DFS Management (SMB-In)",
"Profiles": "NET_FW_PROFILE2_ALL",
"RemoteAddresses": "*",
"RuleEnabled": true
},
{
"Action": "NET_FW_ACTION_ALLOW",
"Host": null,
"HostId": 0,
"Id": 0,
"Interfaces": null,
"LocalPorts": "135",
"Name": "RCE allow",
"Profiles": "3",
"RemoteAddresses": "*",
"RuleEnabled": true
},
{
"Action": "NET_FW_ACTION_ALLOW",
"Host": null,
"HostId": 0,
"Id": 0,
"Interfaces": null,
"LocalPorts": "3389",
"Name": "RCE allow",
"Profiles": "3",
"RemoteAddresses": "*",
"RuleEnabled": true
},
{
"Action": "NET_FW_ACTION_ALLOW",
"Host": null,
"HostId": 0,
"Id": 0,
"Interfaces": null,
"LocalPorts": "5985",
"Name": "RCE allow",
"Profiles": "3",
"RemoteAddresses": "*",
"RuleEnabled": true
},
{
"Action": "NET_FW_ACTION_ALLOW",
"Host": null,
"HostId": 0,
"Id": 0,
"Interfaces": null,
"LocalPorts": "139",
"Name": "File and Printer Sharing (NB-Session-In)",
"Profiles": "NET_FW_PROFILE2_DOMAIN",
"RemoteAddresses": "*",
"RuleEnabled": true
},
{
"Action": "NET_FW_ACTION_ALLOW",
"Host": null,
"HostId": 0,
"Id": 0,
"Interfaces": null,
"LocalPorts": "*",
"Name": "Network Discovery for Teredo (UPnP-In)",
"Profiles": "NET_FW_PROFILE2_PUBLIC",
"RemoteAddresses": "*",
"RuleEnabled": true
}
],
"properties": {
"Action": {
"examples": [
"NET_FW_ACTION_ALLOW"
],
"title": "The Action Schema",
"type": "string"
},
"Host": {
"examples": [
null
],
"title": "The Host Schema",
"type": "null"
},
"HostId": {
"examples": [
0
],
"title": "The HostId Schema",
"type": "integer"
},
"Id": {
"examples": [
0
],
"title": "The Id Schema",
"type": "integer"
},
"Interfaces": {
"examples": [
null
],
"title": "The Interfaces Schema",
"type": "null"
},
"LocalPorts": {
"examples": [
"445",
"135",
"3389",
"5985",
"139",
"*"
],
"title": "The LocalPorts Schema",
"type": "string"
},
"Name": {
"examples": [
"DFS Management (SMB-In)",
"RCE allow",
"File and Printer Sharing (NB-Session-In)",
"Network Discovery for Teredo (UPnP-In)"
],
"title": "The Name Schema",
"type": "string"
},
"Profiles": {
"examples": [
"NET_FW_PROFILE2_ALL",
"3",
"NET_FW_PROFILE2_DOMAIN",
"NET_FW_PROFILE2_PUBLIC"
],
"title": "The Profiles Schema",
"type": "string"
},
"RemoteAddresses": {
"examples": [
"*"
],
"title": "The RemoteAddresses Schema",
"type": "string"
},
"RuleEnabled": {
"examples": [
true
],
"title": "The RuleEnabled Schema",
"type": "boolean"
}
},
"required": [
"RuleEnabled",
"HostId",
"Id",
"Host",
"Profiles",
"Interfaces",
"Action",
"RemoteAddresses",
"LocalPorts",
"Name"
],
"title": "A Schema",
"type": "object"
},
"title": "The WindowsFirewallRule Schema",
"type": "array"
},
"WindowsFirewallSetting": {
"default": {},
"examples": [
{
"DomainProfileDefaultBlockAction": "NET_FW_ACTION_BLOCK",
"DomainProfileEnabled": true,
"Id": 0,
"PrivateProfileDefaultBlockAction": "NET_FW_ACTION_BLOCK",
"PrivateProfileEnabled": true,
"PublicProfileDefaultBlockAction": "NET_FW_ACTION_BLOCK",
"PublicProfileEnabled": true
}
],
"properties": {
"DomainProfileDefaultBlockAction": {
"default": "",
"examples": [
"NET_FW_ACTION_BLOCK"
],
"title": "The DomainProfileDefaultBlockAction Schema",
"type": "string"
},
"DomainProfileEnabled": {
"default": false,
"examples": [
true
],
"title": "The DomainProfileEnabled Schema",
"type": "boolean"
},
"Id": {
"default": 0,
"examples": [
0
],
"title": "The Id Schema",
"type": "integer"
},
"PrivateProfileDefaultBlockAction": {
"default": "",
"examples": [
"NET_FW_ACTION_BLOCK"
],
"title": "The PrivateProfileDefaultBlockAction Schema",
"type": "string"
},
"PrivateProfileEnabled": {
"default": false,
"examples": [
true
],
"title": "The PrivateProfileEnabled Schema",
"type": "boolean"
},
"PublicProfileDefaultBlockAction": {
"default": "",
"examples": [
"NET_FW_ACTION_BLOCK"
],
"title": "The PublicProfileDefaultBlockAction Schema",
"type": "string"
},
"PublicProfileEnabled": {
"default": false,
"examples": [
true
],
"title": "The PublicProfileEnabled Schema",
"type": "boolean"
}
},
"required": [
"DomainProfileEnabled",
"PublicProfileEnabled",
"PrivateProfileEnabled",
"Id",
"DomainProfileDefaultBlockAction",
"PublicProfileDefaultBlockAction",
"PrivateProfileDefaultBlockAction"
],
"title": "The WindowsFirewallSetting Schema",
"type": "object"
},
"WindowsFirewallSettingId": {
"default": 0,
"examples": [
0
],
"title": "The WindowsFirewallSettingId Schema",
"type": "integer"
}
},
"required": [
"IsServerOS",
"WindowsFirewallSettingId",
"Id",
"FileShare",
"TCPConnection",
"WindowsFirewallRule",
"Port",
"Program",
"Role",
"WindowsFirewallSetting",
"NetworkMask",
"IPAddress",
"DNSHostname",
"OperatingSystem"
],
"title": "Root Schema",
"type": "object"
} | Apache-2.0 | en |
captainhook-go/captainhook | 0cb95276265941331b56c3094f1ce673912f0be2 | 2023-11-24T19:41:34 | schema/captainhook.json | 21 | 2024-05-27T09:14:08.349546Z | {
"$defs": {
"action": {
"config": {
"description": "Special settings for an action",
"properties": {
"failure-allowed": {
"description": "Allow this action to fail",
"type": "boolean"
},
"run-async": {
"description": "This action should be executes asynchronously",
"type": "boolean"
},
"working-directory": {
"description": "Define a special working directory for the command to execute",
"type": "string"
}
},
"type": "object"
},
"description": "Action that will be executed",
"properties": {
"options": {
"$ref": "#/$defs/options",
"description": "Options for the command to execute"
},
"run": {
"description": "The command to execute",
"type": "string"
}
},
"required": [
"run"
],
"type": "object"
},
"condition": {
"description": "A command that determines if the action will be executed",
"properties": {
"options": {
"$ref": "#/$defs/options",
"description": "Options for the command to execute"
},
"run": {
"description": "The command to execute",
"type": "string"
}
},
"required": [
"run"
],
"type": "object"
},
"hook": {
"description": "Hook configuration for a specific git hook",
"properties": {
"actions": {
"description": "List of actions to execute if the hook is triggered",
"items": {
"$ref": "#/$defs/action"
},
"type": "array"
}
},
"required": [
"actions"
],
"type": "object"
},
"options": {
"additionalProperties": {
"anyOf": [
{
"type": "string"
},
{
"type": "number"
},
{
"type": "boolean"
},
{
"type": "array"
}
]
},
"description": "Options for Actions or Conditions"
}
},
"$id": "http://captainhook.info/schema/captainhook.json",
"$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "CaptainHook configuration file",
"properties": {
"config": {
"description": "CaptainHook settings",
"properties": {
"ansi-colors": {
"description": "Should colored output be used",
"type": "boolean"
},
"custom": {
"additionalProperties": {
"type": "string"
},
"description": "List of custom key value options",
"type": "object"
},
"fail-on-first-error": {
"description": "Should the execution stop on the first error, or run all action and collect the errors",
"type": "boolean"
},
"git-directory": {
"description": "Path to your .git directory",
"type": "string"
},
"includes": {
"description": "List of config files to include",
"items": {
"type": "string"
},
"type": "array"
},
"run-async": {
"description": "Run actions concurrently or in sequence",
"type": "boolean"
},
"run-path": {
"description": "Path to the captainhook binary, if empty the Cap'n must be in your PATH",
"type": "string"
},
"verbosity": {
"description": "Verbosity of the command use 'verbose' or even 'debug' or more verbose output",
"type": "string"
}
},
"type": "object"
},
"hooks": {
"description": "List of hook configurations",
"properties": {
"commit-msg": {
"$ref": "#/$defs/hook"
},
"post-change": {
"$ref": "#/$defs/hook"
},
"post-checkout": {
"$ref": "#/$defs/hook"
},
"post-commit": {
"$ref": "#/$defs/hook"
},
"post-merge": {
"$ref": "#/$defs/hook"
},
"post-rewrite": {
"$ref": "#/$defs/hook"
},
"pre-commit": {
"$ref": "#/$defs/hook"
},
"pre-push": {
"$ref": "#/$defs/hook"
},
"prepare-commit-msg": {
"$ref": "#/$defs/hook"
}
},
"required": [],
"type": "object"
}
},
"required": [
"hooks"
],
"title": "CaptainHook",
"type": "object"
} | MIT | en |
s3c2/vfcfinder | 720e4568a24e9b8f75f5b1c152c4badd99f43411 | 2023-06-22T21:03:47 | vfcfinder/data/osv_schema.json | 12 | 2024-05-27T04:48:56.499311Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "A schema for describing a vulnerability in an open source package.",
"properties": {
"affected": {
"items": {
"allOf": [
{
"else": {
"required": [
"versions"
]
},
"if": {
"properties": {
"ranges": {
"contains": {
"properties": {
"type": {
"enum": [
"SEMVER",
"ECOSYSTEM"
]
}
}
}
}
}
},
"then": {}
}
],
"properties": {
"database_specific": {
"type": "object"
},
"ecosystem_specific": {
"type": "object"
},
"package": {
"properties": {
"ecosystem": {
"type": "string"
},
"name": {
"type": "string"
},
"purl": {
"type": "string"
}
},
"required": [
"ecosystem",
"name"
],
"type": "object"
},
"ranges": {
"items": {
"allOf": [
{
"if": {
"properties": {
"type": {
"const": "GIT"
}
}
},
"then": {
"required": [
"repo"
]
}
},
{
"if": {
"properties": {
"events": {
"contains": {
"required": [
"last_affected"
]
}
}
}
},
"then": {
"not": {
"properties": {
"events": {
"contains": {
"required": [
"fixed"
]
}
}
}
}
}
}
],
"properties": {
"database_specific": {
"type": "object"
},
"events": {
"contains": {
"required": [
"introduced"
]
},
"items": {
"oneOf": [
{
"properties": {
"introduced": {
"type": "string"
}
},
"required": [
"introduced"
],
"type": "object"
},
{
"properties": {
"fixed": {
"type": "string"
}
},
"required": [
"fixed"
],
"type": "object"
},
{
"properties": {
"last_affected": {
"type": "string"
}
},
"required": [
"last_affected"
],
"type": "object"
},
{
"properties": {
"limit": {
"type": "string"
}
},
"required": [
"limit"
],
"type": "object"
}
],
"type": "object"
},
"minItems": 1,
"type": "array"
},
"repo": {
"type": "string"
},
"type": {
"enum": [
"GIT",
"SEMVER",
"ECOSYSTEM"
],
"type": "string"
}
},
"required": [
"type",
"events"
],
"type": "object"
},
"type": "array"
},
"versions": {
"items": {
"type": "string"
},
"type": "array"
}
},
"type": "object"
},
"type": "array"
},
"aliases": {
"items": {
"type": "string"
},
"type": "array"
},
"credits": {
"items": {
"properties": {
"contact": {
"items": {
"type": "string"
},
"type": "array"
},
"name": {
"type": "string"
}
},
"required": [
"name"
],
"type": "object"
},
"type": "array"
},
"database_specific": {
"type": "object"
},
"details": {
"type": "string"
},
"id": {
"type": "string"
},
"modified": {
"format": "date-time",
"type": "string"
},
"published": {
"format": "date-time",
"type": "string"
},
"references": {
"items": {
"properties": {
"type": {
"enum": [
"ADVISORY",
"ARTICLE",
"REPORT",
"FIX",
"GIT",
"PACKAGE",
"EVIDENCE",
"WEB"
],
"type": "string"
},
"url": {
"format": "uri",
"type": "string"
}
},
"required": [
"type",
"url"
],
"type": "object"
},
"type": "array"
},
"related": {
"items": {
"type": "string"
},
"type": "array"
},
"schema_version": {
"type": "string"
},
"severity": {
"items": {
"properties": {
"score": {
"type": "string"
},
"type": {
"enum": [
"CVSS_V3"
],
"type": "string"
}
},
"required": [
"type",
"score"
],
"type": "object"
},
"type": "array"
},
"summary": {
"type": "string"
},
"withdrawn": {
"format": "date-time",
"type": "string"
}
},
"required": [
"id",
"modified"
],
"title": "Open Source Vulnerability",
"type": "object"
} | Apache-2.0 | en |
s3c2/vfcfinder | 720e4568a24e9b8f75f5b1c152c4badd99f43411 | 2023-06-22T21:03:47 | tests/data/osv_schema.json | 12 | 2024-05-27T04:48:56.499311Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "A schema for describing a vulnerability in an open source package.",
"properties": {
"affected": {
"items": {
"allOf": [
{
"else": {
"required": [
"versions"
]
},
"if": {
"properties": {
"ranges": {
"contains": {
"properties": {
"type": {
"enum": [
"SEMVER",
"ECOSYSTEM"
]
}
}
}
}
}
},
"then": {}
}
],
"properties": {
"database_specific": {
"type": "object"
},
"ecosystem_specific": {
"type": "object"
},
"package": {
"properties": {
"ecosystem": {
"type": "string"
},
"name": {
"type": "string"
},
"purl": {
"type": "string"
}
},
"required": [
"ecosystem",
"name"
],
"type": "object"
},
"ranges": {
"items": {
"allOf": [
{
"if": {
"properties": {
"type": {
"const": "GIT"
}
}
},
"then": {
"required": [
"repo"
]
}
},
{
"if": {
"properties": {
"events": {
"contains": {
"required": [
"last_affected"
]
}
}
}
},
"then": {
"not": {
"properties": {
"events": {
"contains": {
"required": [
"fixed"
]
}
}
}
}
}
}
],
"properties": {
"database_specific": {
"type": "object"
},
"events": {
"contains": {
"required": [
"introduced"
]
},
"items": {
"oneOf": [
{
"properties": {
"introduced": {
"type": "string"
}
},
"required": [
"introduced"
],
"type": "object"
},
{
"properties": {
"fixed": {
"type": "string"
}
},
"required": [
"fixed"
],
"type": "object"
},
{
"properties": {
"last_affected": {
"type": "string"
}
},
"required": [
"last_affected"
],
"type": "object"
},
{
"properties": {
"limit": {
"type": "string"
}
},
"required": [
"limit"
],
"type": "object"
}
],
"type": "object"
},
"minItems": 1,
"type": "array"
},
"repo": {
"type": "string"
},
"type": {
"enum": [
"GIT",
"SEMVER",
"ECOSYSTEM"
],
"type": "string"
}
},
"required": [
"type",
"events"
],
"type": "object"
},
"type": "array"
},
"versions": {
"items": {
"type": "string"
},
"type": "array"
}
},
"type": "object"
},
"type": "array"
},
"aliases": {
"items": {
"type": "string"
},
"type": "array"
},
"credits": {
"items": {
"properties": {
"contact": {
"items": {
"type": "string"
},
"type": "array"
},
"name": {
"type": "string"
}
},
"required": [
"name"
],
"type": "object"
},
"type": "array"
},
"database_specific": {
"type": "object"
},
"details": {
"type": "string"
},
"id": {
"type": "string"
},
"modified": {
"format": "date-time",
"type": "string"
},
"published": {
"format": "date-time",
"type": "string"
},
"references": {
"items": {
"properties": {
"type": {
"enum": [
"ADVISORY",
"ARTICLE",
"REPORT",
"FIX",
"GIT",
"PACKAGE",
"EVIDENCE",
"WEB"
],
"type": "string"
},
"url": {
"format": "uri",
"type": "string"
}
},
"required": [
"type",
"url"
],
"type": "object"
},
"type": "array"
},
"related": {
"items": {
"type": "string"
},
"type": "array"
},
"schema_version": {
"type": "string"
},
"severity": {
"items": {
"properties": {
"score": {
"type": "string"
},
"type": {
"enum": [
"CVSS_V3"
],
"type": "string"
}
},
"required": [
"type",
"score"
],
"type": "object"
},
"type": "array"
},
"summary": {
"type": "string"
},
"withdrawn": {
"format": "date-time",
"type": "string"
}
},
"required": [
"id",
"modified"
],
"title": "Open Source Vulnerability",
"type": "object"
} | Apache-2.0 | en |
Digitaler-Impfnachweis/covpass-ios | 61b67cc432eeb5e2c1909e0d99d108b326277465 | 2021-07-15T12:07:30 | Source/CovPassCommon/Sources/CovPassCommon/Resources/DCC-ValueSets/DCC.combined-schema.json | 94 | 2024-05-28T03:51:40.491349Z | {
"$comment": "Schema version 1.3.0",
"$defs": {
"certificate_id": {
"description": "Certificate Identifier, format as per UVCI: Annex 2 in https://ec.europa.eu/health/sites/health/files/ehealth/docs/vaccination-proof_interoperability-guidelines_en.pdf",
"maxLength": 80,
"type": "string"
},
"country_vt": {
"description": "Country of Vaccination / Test, ISO 3166 alpha-2 where possible",
"pattern": "[A-Z]{1,10}",
"type": "string",
"valueset-uri": "valuesets/country-2-codes.json"
},
"disease-agent-targeted": {
"description": "EU eHealthNetwork: Value Sets for Digital Covid Certificates. version 1.0, 2021-04-16, section 2.1",
"type": "string",
"valueset-uri": "valuesets/disease-agent-targeted.json"
},
"dose_posint": {
"description": "Dose Number / Total doses in Series: positive integer",
"minimum": 1,
"type": "integer"
},
"issuer": {
"description": "Certificate Issuer",
"maxLength": 80,
"type": "string"
},
"person_name": {
"description": "Person name: Surname(s), forename(s) - in that order",
"properties": {
"fn": {
"description": "The surname or primary name(s) of the person addressed in the certificate",
"examples": [
"d'\u010cervenkov\u00e1 Panklov\u00e1"
],
"maxLength": 80,
"title": "Surname",
"type": "string"
},
"fnt": {
"description": "The surname(s) of the person, transliterated ICAO 9303",
"examples": [
"DCERVENKOVA<PANKLOVA"
],
"maxLength": 80,
"pattern": "^[A-Z<]*$",
"title": "Standardised surname",
"type": "string"
},
"gn": {
"description": "The forename(s) of the person addressed in the certificate",
"examples": [
"Ji\u0159ina-Maria Alena"
],
"maxLength": 80,
"title": "Forename",
"type": "string"
},
"gnt": {
"description": "The forename(s) of the person, transliterated ICAO 9303",
"examples": [
"JIRINA<MARIA<ALENA"
],
"maxLength": 80,
"pattern": "^[A-Z<]*$",
"title": "Standardised forename",
"type": "string"
}
},
"required": [
"fnt"
],
"type": "object"
},
"recovery_entry": {
"description": "Recovery Entry",
"properties": {
"ci": {
"$ref": "#/$defs/certificate_id",
"description": "Unique Certificate Identifier, UVCI"
},
"co": {
"$ref": "#/$defs/country_vt",
"description": "Country of Test"
},
"df": {
"description": "ISO 8601 complete date: Certificate Valid From",
"format": "date",
"type": "string"
},
"du": {
"description": "ISO 8601 complete date: Certificate Valid Until",
"format": "date",
"type": "string"
},
"fr": {
"description": "ISO 8601 complete date of first positive NAA test result",
"format": "date",
"type": "string"
},
"is": {
"$ref": "#/$defs/issuer",
"description": "Certificate Issuer"
},
"tg": {
"$ref": "#/$defs/disease-agent-targeted"
}
},
"required": [
"tg",
"fr",
"co",
"is",
"df",
"du",
"ci"
],
"type": "object"
},
"test-manf": {
"description": "EU eHealthNetwork: Value Sets for Digital Covid Certificates. version 1.0, 2021-04-16, section 2.8",
"type": "string",
"valueset-uri": "valuesets/test-manf.json"
},
"test-result": {
"description": "EU eHealthNetwork: Value Sets for Digital Covid Certificates. version 1.0, 2021-04-16, section 2.9",
"type": "string",
"valueset-uri": "valuesets/test-result.json"
},
"test-type": {
"description": "EU eHealthNetwork: Value Sets for Digital Covid Certificates. version 1.0, 2021-04-16, section 2.7",
"type": "string",
"valueset-uri": "valuesets/test-type.json"
},
"test_entry": {
"description": "Test Entry",
"properties": {
"ci": {
"$ref": "#/$defs/certificate_id",
"description": "Unique Certificate Identifier, UVCI"
},
"co": {
"$ref": "#/$defs/country_vt",
"description": "Country of Test"
},
"is": {
"$ref": "#/$defs/issuer",
"description": "Certificate Issuer"
},
"ma": {
"$ref": "#/$defs/test-manf",
"description": "RAT Test name and manufacturer"
},
"nm": {
"description": "NAA Test Name",
"maxLength": 80,
"type": "string"
},
"sc": {
"description": "Date/Time of Sample Collection",
"format": "date-time",
"type": "string"
},
"tc": {
"description": "Testing Centre",
"maxLength": 80,
"type": "string"
},
"tg": {
"$ref": "#/$defs/disease-agent-targeted"
},
"tr": {
"$ref": "#/$defs/test-result",
"description": "Test Result"
},
"tt": {
"$ref": "#/$defs/test-type",
"description": "Type of Test"
}
},
"required": [
"tg",
"tt",
"sc",
"tr",
"co",
"is",
"ci"
],
"type": "object"
},
"vaccination_entry": {
"description": "Vaccination Entry",
"properties": {
"ci": {
"$ref": "#/$defs/certificate_id",
"description": "Unique Certificate Identifier: UVCI"
},
"co": {
"$ref": "#/$defs/country_vt",
"description": "Country of Vaccination"
},
"dn": {
"$ref": "#/$defs/dose_posint",
"description": "Dose Number"
},
"dt": {
"description": "ISO8601 complete date: Date of Vaccination",
"format": "date",
"type": "string"
},
"is": {
"$ref": "#/$defs/issuer",
"description": "Certificate Issuer"
},
"ma": {
"$ref": "#/$defs/vaccine-mah-manf",
"description": "Marketing Authorization Holder - if no MAH present, then manufacturer"
},
"mp": {
"$ref": "#/$defs/vaccine-medicinal-product",
"description": "vaccine medicinal product"
},
"sd": {
"$ref": "#/$defs/dose_posint",
"description": "Total Series of Doses"
},
"tg": {
"$ref": "#/$defs/disease-agent-targeted",
"description": "disease or agent targeted"
},
"vp": {
"$ref": "#/$defs/vaccine-prophylaxis",
"description": "vaccine or prophylaxis"
}
},
"required": [
"tg",
"vp",
"mp",
"ma",
"dn",
"sd",
"dt",
"co",
"is",
"ci"
],
"type": "object"
},
"vaccine-mah-manf": {
"description": "EU eHealthNetwork: Value Sets for Digital Covid Certificates. version 1.0, 2021-04-16, section 2.4",
"type": "string",
"valueset-uri": "valuesets/vaccine-mah-manf.json"
},
"vaccine-medicinal-product": {
"description": "EU eHealthNetwork: Value Sets for Digital Covid Certificates. version 1.0, 2021-04-16, section 2.3",
"type": "string",
"valueset-uri": "valuesets/vaccine-medicinal-product.json"
},
"vaccine-prophylaxis": {
"description": "EU eHealthNetwork: Value Sets for Digital Covid Certificates. version 1.0, 2021-04-16, section 2.2",
"type": "string",
"valueset-uri": "valuesets/vaccine-prophylaxis.json"
}
},
"$id": "https://id.uvci.eu/DCC.combined-schema.json",
"$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "EU Digital Covid Certificate",
"oneOf": [
{
"required": [
"ver",
"nam",
"dob",
"v"
]
},
{
"required": [
"ver",
"nam",
"dob",
"t"
]
},
{
"required": [
"ver",
"nam",
"dob",
"r"
]
}
],
"properties": {
"dob": {
"description": "Date of Birth of the person addressed in the DCC. ISO 8601 date format restricted to range 1900-2099 or empty",
"examples": [
"1979-04-14",
"1950",
"1901-08",
""
],
"pattern": "^((19|20)\\d\\d(-\\d\\d){0,2}){0,1}$",
"title": "Date of birth",
"type": "string"
},
"nam": {
"$ref": "#/$defs/person_name",
"description": "Surname(s), forename(s) - in that order"
},
"r": {
"description": "Recovery Group",
"items": {
"$ref": "#/$defs/recovery_entry"
},
"maxItems": 1,
"minItems": 1,
"type": "array"
},
"t": {
"description": "Test Group",
"items": {
"$ref": "#/$defs/test_entry"
},
"maxItems": 1,
"minItems": 1,
"type": "array"
},
"v": {
"description": "Vaccination Group",
"items": {
"$ref": "#/$defs/vaccination_entry"
},
"maxItems": 1,
"minItems": 1,
"type": "array"
},
"ver": {
"description": "Version of the schema, according to Semantic versioning (ISO, https://semver.org/ version 2.0.0 or newer)",
"examples": [
"1.3.0"
],
"pattern": "^\\d+.\\d+.\\d+$",
"title": "Schema version",
"type": "string"
}
},
"title": "EU DCC",
"type": "object"
} | Apache-2.0 | en |
Digitaler-Impfnachweis/certification-apis | 14a52d0e38c38ebdfd484e4be236e8aeca379a92 | 2021-07-01T09:24:16 | DCC.combined-schema.json | 175 | 2024-05-28T02:57:31.698945Z | {
"$comment": "Schema version 1.3.0",
"$defs": {
"certificate_id": {
"description": "Certificate Identifier, format as per UVCI: Annex 2 in https://ec.europa.eu/health/sites/health/files/ehealth/docs/vaccination-proof_interoperability-guidelines_en.pdf",
"maxLength": 80,
"type": "string"
},
"country_vt": {
"description": "Country of Vaccination / Test, ISO 3166 alpha-2 where possible",
"pattern": "[A-Z]{1,10}",
"type": "string",
"valueset-uri": "valuesets/country-2-codes.json"
},
"disease-agent-targeted": {
"description": "EU eHealthNetwork: Value Sets for Digital Covid Certificates. version 1.0, 2021-04-16, section 2.1",
"type": "string",
"valueset-uri": "valuesets/disease-agent-targeted.json"
},
"dose_posint": {
"description": "Dose Number / Total doses in Series: positive integer",
"minimum": 1,
"type": "integer"
},
"issuer": {
"description": "Certificate Issuer",
"maxLength": 80,
"type": "string"
},
"person_name": {
"description": "Person name: Surname(s), forename(s) - in that order",
"properties": {
"fn": {
"description": "The surname or primary name(s) of the person addressed in the certificate",
"examples": [
"d'\u010cervenkov\u00e1 Panklov\u00e1"
],
"maxLength": 80,
"title": "Surname",
"type": "string"
},
"fnt": {
"description": "The surname(s) of the person, transliterated ICAO 9303",
"examples": [
"DCERVENKOVA<PANKLOVA"
],
"maxLength": 80,
"pattern": "^[A-Z<]*$",
"title": "Standardised surname",
"type": "string"
},
"gn": {
"description": "The forename(s) of the person addressed in the certificate",
"examples": [
"Ji\u0159ina-Maria Alena"
],
"maxLength": 80,
"title": "Forename",
"type": "string"
},
"gnt": {
"description": "The forename(s) of the person, transliterated ICAO 9303",
"examples": [
"JIRINA<MARIA<ALENA"
],
"maxLength": 80,
"pattern": "^[A-Z<]*$",
"title": "Standardised forename",
"type": "string"
}
},
"required": [
"fnt"
],
"type": "object"
},
"recovery_entry": {
"description": "Recovery Entry",
"properties": {
"ci": {
"$ref": "#/$defs/certificate_id",
"description": "Unique Certificate Identifier, UVCI"
},
"co": {
"$ref": "#/$defs/country_vt",
"description": "Country of Test"
},
"df": {
"description": "ISO 8601 complete date: Certificate Valid From",
"format": "date",
"type": "string"
},
"du": {
"description": "ISO 8601 complete date: Certificate Valid Until",
"format": "date",
"type": "string"
},
"fr": {
"description": "ISO 8601 complete date of first positive NAA test result",
"format": "date",
"type": "string"
},
"is": {
"$ref": "#/$defs/issuer",
"description": "Certificate Issuer"
},
"tg": {
"$ref": "#/$defs/disease-agent-targeted"
}
},
"required": [
"tg",
"fr",
"co",
"is",
"df",
"du",
"ci"
],
"type": "object"
},
"test-manf": {
"description": "EU eHealthNetwork: Value Sets for Digital Covid Certificates. version 1.0, 2021-04-16, section 2.8",
"type": "string",
"valueset-uri": "valuesets/test-manf.json"
},
"test-result": {
"description": "EU eHealthNetwork: Value Sets for Digital Covid Certificates. version 1.0, 2021-04-16, section 2.9",
"type": "string",
"valueset-uri": "valuesets/test-result.json"
},
"test-type": {
"description": "EU eHealthNetwork: Value Sets for Digital Covid Certificates. version 1.0, 2021-04-16, section 2.7",
"type": "string",
"valueset-uri": "valuesets/test-type.json"
},
"test_entry": {
"description": "Test Entry",
"properties": {
"ci": {
"$ref": "#/$defs/certificate_id",
"description": "Unique Certificate Identifier, UVCI"
},
"co": {
"$ref": "#/$defs/country_vt",
"description": "Country of Test"
},
"is": {
"$ref": "#/$defs/issuer",
"description": "Certificate Issuer"
},
"ma": {
"$ref": "#/$defs/test-manf",
"description": "RAT Test name and manufacturer"
},
"nm": {
"description": "NAA Test Name",
"maxLength": 80,
"type": "string"
},
"sc": {
"description": "Date/Time of Sample Collection",
"format": "date-time",
"type": "string"
},
"tc": {
"description": "Testing Centre",
"maxLength": 80,
"type": "string"
},
"tg": {
"$ref": "#/$defs/disease-agent-targeted"
},
"tr": {
"$ref": "#/$defs/test-result",
"description": "Test Result"
},
"tt": {
"$ref": "#/$defs/test-type",
"description": "Type of Test"
}
},
"required": [
"tg",
"tt",
"sc",
"tr",
"co",
"is",
"ci"
],
"type": "object"
},
"vaccination_entry": {
"description": "Vaccination Entry",
"properties": {
"ci": {
"$ref": "#/$defs/certificate_id",
"description": "Unique Certificate Identifier: UVCI"
},
"co": {
"$ref": "#/$defs/country_vt",
"description": "Country of Vaccination"
},
"dn": {
"$ref": "#/$defs/dose_posint",
"description": "Dose Number"
},
"dt": {
"description": "ISO8601 complete date: Date of Vaccination",
"format": "date",
"type": "string"
},
"is": {
"$ref": "#/$defs/issuer",
"description": "Certificate Issuer"
},
"ma": {
"$ref": "#/$defs/vaccine-mah-manf",
"description": "Marketing Authorization Holder - if no MAH present, then manufacturer"
},
"mp": {
"$ref": "#/$defs/vaccine-medicinal-product",
"description": "vaccine medicinal product"
},
"sd": {
"$ref": "#/$defs/dose_posint",
"description": "Total Series of Doses"
},
"tg": {
"$ref": "#/$defs/disease-agent-targeted",
"description": "disease or agent targeted"
},
"vp": {
"$ref": "#/$defs/vaccine-prophylaxis",
"description": "vaccine or prophylaxis"
}
},
"required": [
"tg",
"vp",
"mp",
"ma",
"dn",
"sd",
"dt",
"co",
"is",
"ci"
],
"type": "object"
},
"vaccine-mah-manf": {
"description": "EU eHealthNetwork: Value Sets for Digital Covid Certificates. version 1.0, 2021-04-16, section 2.4",
"type": "string",
"valueset-uri": "valuesets/vaccine-mah-manf.json"
},
"vaccine-medicinal-product": {
"description": "EU eHealthNetwork: Value Sets for Digital Covid Certificates. version 1.0, 2021-04-16, section 2.3",
"type": "string",
"valueset-uri": "valuesets/vaccine-medicinal-product.json"
},
"vaccine-prophylaxis": {
"description": "EU eHealthNetwork: Value Sets for Digital Covid Certificates. version 1.0, 2021-04-16, section 2.2",
"type": "string",
"valueset-uri": "valuesets/vaccine-prophylaxis.json"
}
},
"$id": "https://id.uvci.eu/DCC.combined-schema.json",
"$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "EU Digital Covid Certificate",
"oneOf": [
{
"required": [
"ver",
"nam",
"dob",
"v"
]
},
{
"required": [
"ver",
"nam",
"dob",
"t"
]
},
{
"required": [
"ver",
"nam",
"dob",
"r"
]
}
],
"properties": {
"dob": {
"description": "Date of Birth of the person addressed in the DCC. ISO 8601 date format restricted to range 1900-2099 or empty",
"examples": [
"1979-04-14",
"1950",
"1901-08",
""
],
"pattern": "^((19|20)\\d\\d(-\\d\\d){0,2}){0,1}$",
"title": "Date of birth",
"type": "string"
},
"nam": {
"$ref": "#/$defs/person_name",
"description": "Surname(s), forename(s) - in that order"
},
"r": {
"description": "Recovery Group",
"items": {
"$ref": "#/$defs/recovery_entry"
},
"maxItems": 1,
"minItems": 1,
"type": "array"
},
"t": {
"description": "Test Group",
"items": {
"$ref": "#/$defs/test_entry"
},
"maxItems": 1,
"minItems": 1,
"type": "array"
},
"v": {
"description": "Vaccination Group",
"items": {
"$ref": "#/$defs/vaccination_entry"
},
"maxItems": 1,
"minItems": 1,
"type": "array"
},
"ver": {
"description": "Version of the schema, according to Semantic versioning (ISO, https://semver.org/ version 2.0.0 or newer)",
"examples": [
"1.3.0"
],
"pattern": "^\\d+.\\d+.\\d+$",
"title": "Schema version",
"type": "string"
}
},
"title": "EU DCC",
"type": "object"
} | Apache-2.0 | en |
Digitaler-Impfnachweis/certification-apis | 96d6f6cc7151e529f0c8396ab3db81b8c542f95c | 2022-07-11T14:59:16 | DCC.combined-schema.json | 175 | 2024-05-28T02:57:31.698945Z | {
"$comment": "Schema version 1.3.2",
"$defs": {
"certificate_id": {
"description": "Certificate Identifier, format as per UVCI: Annex 2 in https://ec.europa.eu/health/sites/health/files/ehealth/docs/vaccination-proof_interoperability-guidelines_en.pdf",
"maxLength": 80,
"type": "string"
},
"country_vt": {
"description": "Country of Vaccination / Test, ISO 3166 alpha-2 where possible",
"pattern": "[A-Z]{1,10}",
"type": "string",
"valueset-uri": "valuesets/country-2-codes.json"
},
"disease-agent-targeted": {
"description": "EU eHealthNetwork: Value Sets for Digital Covid Certificates. version 1.0, 2021-04-16, section 2.1",
"type": "string",
"valueset-uri": "valuesets/disease-agent-targeted.json"
},
"dose_posint": {
"description": "Dose Number / Total doses in Series: positive integer",
"minimum": 1,
"type": "integer"
},
"issuer": {
"description": "Certificate Issuer",
"maxLength": 80,
"type": "string"
},
"person_name": {
"anyOf": [
{
"required": [
"fnt"
]
},
{
"required": [
"gnt"
]
}
],
"description": "Person name: Surname(s), forename(s) - in that order",
"properties": {
"fn": {
"description": "The surname or primary name(s) of the person addressed in the certificate",
"examples": [
"d'\u010cervenkov\u00e1 Panklov\u00e1"
],
"maxLength": 80,
"title": "Surname",
"type": "string"
},
"fnt": {
"description": "The surname(s) of the person, transliterated ICAO 9303",
"examples": [
"DCERVENKOVA<PANKLOVA"
],
"maxLength": 80,
"pattern": "^[A-Z<]*$",
"title": "Standardised surname",
"type": "string"
},
"gn": {
"description": "The forename(s) of the person addressed in the certificate",
"examples": [
"Ji\u0159ina-Maria Alena"
],
"maxLength": 80,
"title": "Forename",
"type": "string"
},
"gnt": {
"description": "The forename(s) of the person, transliterated ICAO 9303",
"examples": [
"JIRINA<MARIA<ALENA"
],
"maxLength": 80,
"pattern": "^[A-Z<]*$",
"title": "Standardised forename",
"type": "string"
}
},
"type": "object"
},
"recovery_entry": {
"description": "Recovery Entry",
"properties": {
"ci": {
"$ref": "#/$defs/certificate_id",
"description": "Unique Certificate Identifier, UVCI"
},
"co": {
"$ref": "#/$defs/country_vt",
"description": "Country of Test"
},
"df": {
"description": "ISO 8601 complete date: Certificate Valid From",
"format": "date",
"type": "string"
},
"du": {
"description": "ISO 8601 complete date: Certificate Valid Until",
"format": "date",
"type": "string"
},
"fr": {
"description": "ISO 8601 complete date of first positive NAA test result",
"format": "date",
"type": "string"
},
"is": {
"$ref": "#/$defs/issuer",
"description": "Certificate Issuer"
},
"tg": {
"$ref": "#/$defs/disease-agent-targeted",
"description": "disease or agent targeted"
}
},
"required": [
"tg",
"fr",
"co",
"is",
"df",
"du",
"ci"
],
"type": "object"
},
"test-manf": {
"description": "EU eHealthNetwork: Value Sets for Digital Covid Certificates. version 1.0, 2021-04-16, section 2.8",
"type": "string",
"valueset-uri": "valuesets/test-manf.json"
},
"test-result": {
"description": "EU eHealthNetwork: Value Sets for Digital Covid Certificates. version 1.0, 2021-04-16, section 2.9",
"type": "string",
"valueset-uri": "valuesets/test-result.json"
},
"test-type": {
"description": "EU eHealthNetwork: Value Sets for Digital Covid Certificates. version 1.0, 2021-04-16, section 2.7",
"type": "string",
"valueset-uri": "valuesets/test-type.json"
},
"test_entry": {
"description": "Test Entry",
"properties": {
"ci": {
"$ref": "#/$defs/certificate_id",
"description": "Unique Certificate Identifier, UVCI"
},
"co": {
"$ref": "#/$defs/country_vt",
"description": "Country of Test"
},
"is": {
"$ref": "#/$defs/issuer",
"description": "Certificate Issuer"
},
"ma": {
"$ref": "#/$defs/test-manf",
"description": "RAT Test name and manufacturer"
},
"nm": {
"description": "NAA Test Name",
"maxLength": 80,
"type": "string"
},
"sc": {
"description": "Date/Time of Sample Collection",
"format": "date-time",
"type": "string"
},
"tc": {
"description": "Testing Centre",
"maxLength": 80,
"type": "string"
},
"tg": {
"$ref": "#/$defs/disease-agent-targeted",
"description": "disease or agent targeted"
},
"tr": {
"$ref": "#/$defs/test-result",
"description": "Test Result"
},
"tt": {
"$ref": "#/$defs/test-type",
"description": "Type of Test"
}
},
"required": [
"tg",
"tt",
"sc",
"tr",
"co",
"is",
"ci"
],
"type": "object"
},
"vaccination_entry": {
"description": "Vaccination Entry",
"properties": {
"ci": {
"$ref": "#/$defs/certificate_id",
"description": "Unique Certificate Identifier: UVCI"
},
"co": {
"$ref": "#/$defs/country_vt",
"description": "Country of Vaccination"
},
"dn": {
"$ref": "#/$defs/dose_posint",
"description": "Dose Number"
},
"dt": {
"description": "ISO8601 complete date: Date of Vaccination",
"format": "date",
"type": "string"
},
"is": {
"$ref": "#/$defs/issuer",
"description": "Certificate Issuer"
},
"ma": {
"$ref": "#/$defs/vaccine-mah-manf",
"description": "Marketing Authorization Holder - if no MAH present, then manufacturer"
},
"mp": {
"$ref": "#/$defs/vaccine-medicinal-product",
"description": "vaccine medicinal product"
},
"sd": {
"$ref": "#/$defs/dose_posint",
"description": "Total Series of Doses"
},
"tg": {
"$ref": "#/$defs/disease-agent-targeted",
"description": "disease or agent targeted"
},
"vp": {
"$ref": "#/$defs/vaccine-prophylaxis",
"description": "vaccine or prophylaxis"
}
},
"required": [
"tg",
"vp",
"mp",
"ma",
"dn",
"sd",
"dt",
"co",
"is",
"ci"
],
"type": "object"
},
"vaccine-mah-manf": {
"description": "EU eHealthNetwork: Value Sets for Digital Covid Certificates. version 1.0, 2021-04-16, section 2.4",
"type": "string",
"valueset-uri": "valuesets/vaccine-mah-manf.json"
},
"vaccine-medicinal-product": {
"description": "EU eHealthNetwork: Value Sets for Digital Covid Certificates. version 1.0, 2021-04-16, section 2.3",
"type": "string",
"valueset-uri": "valuesets/vaccine-medicinal-product.json"
},
"vaccine-prophylaxis": {
"description": "EU eHealthNetwork: Value Sets for Digital Covid Certificates. version 1.0, 2021-04-16, section 2.2",
"type": "string",
"valueset-uri": "valuesets/vaccine-prophylaxis.json"
}
},
"$id": "https://id.uvci.eu/DCC.combined-schema.json",
"$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "EU Digital Covid Certificate",
"oneOf": [
{
"required": [
"ver",
"nam",
"dob",
"v"
]
},
{
"required": [
"ver",
"nam",
"dob",
"t"
]
},
{
"required": [
"ver",
"nam",
"dob",
"r"
]
}
],
"properties": {
"dob": {
"description": "Date of Birth of the person addressed in the DCC. ISO 8601 date format restricted to range 1900-2099 or empty",
"examples": [
"1979-04-14",
"1950",
"1901-08",
""
],
"pattern": "^((19|20)\\d\\d(-\\d\\d){0,2}){0,1}$",
"title": "Date of birth",
"type": "string"
},
"nam": {
"$ref": "#/$defs/person_name",
"description": "Surname(s), forename(s) - in that order"
},
"r": {
"description": "Recovery Group",
"items": {
"$ref": "#/$defs/recovery_entry"
},
"maxItems": 1,
"minItems": 1,
"type": "array"
},
"t": {
"description": "Test Group",
"items": {
"$ref": "#/$defs/test_entry"
},
"maxItems": 1,
"minItems": 1,
"type": "array"
},
"v": {
"description": "Vaccination Group",
"items": {
"$ref": "#/$defs/vaccination_entry"
},
"maxItems": 1,
"minItems": 1,
"type": "array"
},
"ver": {
"description": "Version of the schema, according to Semantic versioning (ISO, https://semver.org/ version 2.0.0 or newer)",
"examples": [
"1.0.0",
"1.3.0",
"1.3.1",
"1.3.2"
],
"pattern": "^\\d+.\\d+.\\d+$",
"title": "Schema version",
"type": "string"
}
},
"title": "EU DCC",
"type": "object"
} | Apache-2.0 | en |
Digitaler-Impfnachweis/covpass-android | 876413bc7c25501c828056e161ba5ccb3efe8efb | 2021-09-15T13:33:38 | covpass-sdk/src/main/assets/covpass-sdk/json-schema-v1.json | 183 | 2024-05-28T03:45:56.084272Z | {
"$comment": "Schema version 1.3.0",
"$defs": {
"certificate_id": {
"description": "Certificate Identifier, format as per UVCI: Annex 2 in https://ec.europa.eu/health/sites/health/files/ehealth/docs/vaccination-proof_interoperability-guidelines_en.pdf",
"maxLength": 80,
"type": "string"
},
"country_vt": {
"description": "Country of Vaccination / Test, ISO 3166 alpha-2 where possible",
"pattern": "[A-Z]{1,10}",
"type": "string",
"valueset-uri": "valuesets/country-2-codes.json"
},
"disease-agent-targeted": {
"description": "EU eHealthNetwork: Value Sets for Digital Covid Certificates. version 1.0, 2021-04-16, section 2.1",
"type": "string",
"valueset-uri": "valuesets/disease-agent-targeted.json"
},
"dose_posint": {
"description": "Dose Number / Total doses in Series: positive integer",
"minimum": 1,
"type": "integer"
},
"issuer": {
"description": "Certificate Issuer",
"maxLength": 80,
"type": "string"
},
"person_name": {
"description": "Person name: Surname(s), forename(s) - in that order",
"properties": {
"fn": {
"description": "The surname or primary name(s) of the person addressed in the certificate",
"examples": [
"d'\u010cervenkov\u00e1 Panklov\u00e1"
],
"maxLength": 80,
"title": "Surname",
"type": "string"
},
"fnt": {
"description": "The surname(s) of the person, transliterated ICAO 9303",
"examples": [
"DCERVENKOVA<PANKLOVA"
],
"maxLength": 80,
"pattern": "^[A-Z<]*$",
"title": "Standardised surname",
"type": "string"
},
"gn": {
"description": "The forename(s) of the person addressed in the certificate",
"examples": [
"Ji\u0159ina-Maria Alena"
],
"maxLength": 80,
"title": "Forename",
"type": "string"
},
"gnt": {
"description": "The forename(s) of the person, transliterated ICAO 9303",
"examples": [
"JIRINA<MARIA<ALENA"
],
"maxLength": 80,
"pattern": "^[A-Z<]*$",
"title": "Standardised forename",
"type": "string"
}
},
"required": [
"fnt"
],
"type": "object"
},
"recovery_entry": {
"description": "Recovery Entry",
"properties": {
"ci": {
"$ref": "#/$defs/certificate_id",
"description": "Unique Certificate Identifier, UVCI"
},
"co": {
"$ref": "#/$defs/country_vt",
"description": "Country of Test"
},
"df": {
"description": "ISO 8601 complete date: Certificate Valid From",
"format": "date",
"type": "string"
},
"du": {
"description": "ISO 8601 complete date: Certificate Valid Until",
"format": "date",
"type": "string"
},
"fr": {
"description": "ISO 8601 complete date of first positive NAA test result",
"format": "date",
"type": "string"
},
"is": {
"$ref": "#/$defs/issuer",
"description": "Certificate Issuer"
},
"tg": {
"$ref": "#/$defs/disease-agent-targeted"
}
},
"required": [
"tg",
"fr",
"co",
"is",
"df",
"du",
"ci"
],
"type": "object"
},
"test-manf": {
"description": "EU eHealthNetwork: Value Sets for Digital Covid Certificates. version 1.0, 2021-04-16, section 2.8",
"type": "string",
"valueset-uri": "valuesets/test-manf.json"
},
"test-result": {
"description": "EU eHealthNetwork: Value Sets for Digital Covid Certificates. version 1.0, 2021-04-16, section 2.9",
"type": "string",
"valueset-uri": "valuesets/test-result.json"
},
"test-type": {
"description": "EU eHealthNetwork: Value Sets for Digital Covid Certificates. version 1.0, 2021-04-16, section 2.7",
"type": "string",
"valueset-uri": "valuesets/test-type.json"
},
"test_entry": {
"description": "Test Entry",
"properties": {
"ci": {
"$ref": "#/$defs/certificate_id",
"description": "Unique Certificate Identifier, UVCI"
},
"co": {
"$ref": "#/$defs/country_vt",
"description": "Country of Test"
},
"is": {
"$ref": "#/$defs/issuer",
"description": "Certificate Issuer"
},
"ma": {
"$ref": "#/$defs/test-manf",
"description": "RAT Test name and manufacturer"
},
"nm": {
"description": "NAA Test Name",
"maxLength": 80,
"type": "string"
},
"sc": {
"description": "Date/Time of Sample Collection",
"format": "date-time",
"type": "string"
},
"tc": {
"description": "Testing Centre",
"maxLength": 80,
"type": "string"
},
"tg": {
"$ref": "#/$defs/disease-agent-targeted"
},
"tr": {
"$ref": "#/$defs/test-result",
"description": "Test Result"
},
"tt": {
"$ref": "#/$defs/test-type",
"description": "Type of Test"
}
},
"required": [
"tg",
"tt",
"sc",
"tr",
"co",
"is",
"ci"
],
"type": "object"
},
"vaccination_entry": {
"description": "Vaccination Entry",
"properties": {
"ci": {
"$ref": "#/$defs/certificate_id",
"description": "Unique Certificate Identifier: UVCI"
},
"co": {
"$ref": "#/$defs/country_vt",
"description": "Country of Vaccination"
},
"dn": {
"$ref": "#/$defs/dose_posint",
"description": "Dose Number"
},
"dt": {
"description": "ISO8601 complete date: Date of Vaccination",
"format": "date",
"type": "string"
},
"is": {
"$ref": "#/$defs/issuer",
"description": "Certificate Issuer"
},
"ma": {
"$ref": "#/$defs/vaccine-mah-manf",
"description": "Marketing Authorization Holder - if no MAH present, then manufacturer"
},
"mp": {
"$ref": "#/$defs/vaccine-medicinal-product",
"description": "vaccine medicinal product"
},
"sd": {
"$ref": "#/$defs/dose_posint",
"description": "Total Series of Doses"
},
"tg": {
"$ref": "#/$defs/disease-agent-targeted",
"description": "disease or agent targeted"
},
"vp": {
"$ref": "#/$defs/vaccine-prophylaxis",
"description": "vaccine or prophylaxis"
}
},
"required": [
"tg",
"vp",
"mp",
"ma",
"dn",
"sd",
"dt",
"co",
"is",
"ci"
],
"type": "object"
},
"vaccine-mah-manf": {
"description": "EU eHealthNetwork: Value Sets for Digital Covid Certificates. version 1.0, 2021-04-16, section 2.4",
"type": "string",
"valueset-uri": "valuesets/vaccine-mah-manf.json"
},
"vaccine-medicinal-product": {
"description": "EU eHealthNetwork: Value Sets for Digital Covid Certificates. version 1.0, 2021-04-16, section 2.3",
"type": "string",
"valueset-uri": "valuesets/vaccine-medicinal-product.json"
},
"vaccine-prophylaxis": {
"description": "EU eHealthNetwork: Value Sets for Digital Covid Certificates. version 1.0, 2021-04-16, section 2.2",
"type": "string",
"valueset-uri": "valuesets/vaccine-prophylaxis.json"
}
},
"$id": "https://id.uvci.eu/DCC.combined-schema.json",
"$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "EU Digital Covid Certificate",
"oneOf": [
{
"required": [
"ver",
"nam",
"dob",
"v"
]
},
{
"required": [
"ver",
"nam",
"dob",
"t"
]
},
{
"required": [
"ver",
"nam",
"dob",
"r"
]
}
],
"properties": {
"dob": {
"description": "Date of Birth of the person addressed in the DCC. ISO 8601 date format restricted to range 1900-2099 or empty",
"examples": [
"1979-04-14",
"1950",
"1901-08",
""
],
"pattern": "^((19|20)\\d\\d(-\\d\\d){0,2}){0,1}$",
"title": "Date of birth",
"type": "string"
},
"nam": {
"$ref": "#/$defs/person_name",
"description": "Surname(s), forename(s) - in that order"
},
"r": {
"description": "Recovery Group",
"items": {
"$ref": "#/$defs/recovery_entry"
},
"maxItems": 1,
"minItems": 1,
"type": "array"
},
"t": {
"description": "Test Group",
"items": {
"$ref": "#/$defs/test_entry"
},
"maxItems": 1,
"minItems": 1,
"type": "array"
},
"v": {
"description": "Vaccination Group",
"items": {
"$ref": "#/$defs/vaccination_entry"
},
"maxItems": 1,
"minItems": 1,
"type": "array"
},
"ver": {
"description": "Version of the schema, according to Semantic versioning (ISO, https://semver.org/ version 2.0.0 or newer)",
"examples": [
"1.3.0"
],
"pattern": "^\\d+.\\d+.\\d+$",
"title": "Schema version",
"type": "string"
}
},
"title": "EU DCC",
"type": "object"
} | Apache-2.0 | en |
ga4gh-beacon/beacon-v2 | 030747a0ef492bd79dc53d3eaf9f6c16ceae236a | 2022-02-22T13:50:28 | framework/json/responses/examples-fullDocuments/beaconBooleanResponse-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"meta": {
"apiVersion": "v2.0",
"beaconId": "org.example.beacon.v2",
"receivedRequestSummary": {
"apiVersion": "2.0",
"pagination": {
"limit": 10,
"skip": 0
},
"requestedSchemas": [
{
"entityType": "EntryTypeB",
"schema": "entry-typeB-schema-v1.0"
}
]
},
"returnedSchemas": [
{
"entityType": "EntryTypeB",
"schema": "entry-typeB-schema-v1.0"
}
]
},
"responseSummary": {
"exists": true
}
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 030747a0ef492bd79dc53d3eaf9f6c16ceae236a | 2022-02-22T13:50:28 | framework/json/responses/examples-sections/beaconBooleanResponseSection-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"exists": true
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 3e6093cf1b20ac74bc021c315511094f930be1ef | 2022-02-22T11:21:39 | framework/json/responses/examples-sections/beaconResultsets-MID-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"resultSets": [
{
"exists": true,
"id": "correctWithResults",
"results": [
{
"id": "BEex1",
"name": "Basic Element example one"
}
],
"resultsCount": 1,
"type": "dataset"
},
{
"exists": false,
"id": "correctWOresults",
"type": "dataset"
}
]
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | c8eae7c9c560d888bdbe111ab8a6d5da8af12d90 | 2022-08-09T16:00:21 | framework/json/responses/beaconErrorResponse.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"description": "An unsuccessful operation.",
"properties": {
"error": {
"$ref": "../common/beaconCommonComponents.json#/definitions/BeaconError",
"description": "Error response"
},
"meta": {
"$ref": "./sections/beaconResponseMeta.json",
"description": "Information about the response that could be relevant for the Beacon client in order to interpret the results."
}
},
"required": [
"meta",
"error"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 23d49cc3976a8561dce849fcde90de7ca96772f3 | 2023-06-14T14:22:26 | framework/json/requests/filteringTerms.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"definitions": {
"AlphanumericFilter": {
"description": "Filter results based on operators and values applied to alphanumeric fields.",
"properties": {
"id": {
"description": "Field identfier to be queried.",
"example": "ageOfOnset",
"type": "string"
},
"operator": {
"default": "=",
"description": "Defines how the value relates to the field `id`.",
"enum": [
"=",
"<",
">",
"!",
">=",
"<="
],
"example": ">",
"type": "string"
},
"scope": {
"description": "The entry type to which the filter applies",
"example": "individuals",
"type": "string"
},
"value": {
"description": "Alphanumeric search term to be used within the query which can contain wildcard characters (%) to denote any number of unknown characters. Values can be assocatied with units if applicable.",
"example": "P70Y",
"type": "string"
}
},
"required": [
"id",
"operator",
"value"
],
"type": "object"
},
"CustomFilter": {
"description": "Filter results to include records that contain a custom term defined by this Beacon.",
"properties": {
"id": {
"description": "Custom filter terms should contain a unique identifier.",
"example": "demographic.ethnicity:asian",
"type": "string"
},
"scope": {
"description": "The entry type to which the filter applies",
"example": "individuals",
"type": "string"
}
},
"required": [
"id"
],
"type": "object"
},
"FilteringTerm": {
"anyOf": [
{
"$ref": "#/definitions/OntologyFilter"
},
{
"$ref": "#/definitions/AlphanumericFilter"
},
{
"$ref": "#/definitions/CustomFilter"
}
]
},
"OntologyFilter": {
"description": "Filter results to include records that contain a specific ontology term.",
"properties": {
"id": {
"description": "Term ID to be queried, using CURIE syntax where possible.",
"example": "HP:0002664",
"type": "string"
},
"includeDescendantTerms": {
"default": true,
"description": "Define if the Beacon should implement the ontology hierarchy, thus query the descendant terms of `id`.",
"type": "boolean"
},
"scope": {
"description": "The entry type to which the filter applies",
"example": "biosamples",
"type": "string"
},
"similarity": {
"default": "exact",
"description": "Allow the Beacon to return results which do not match the filter exactly, but do match to a certain degree of similarity. The Beacon defines the semantic similarity model implemented and how to apply the thresholds of 'high', 'medium' and 'low' similarity.",
"enum": [
"exact",
"high",
"medium",
"low"
],
"type": "string"
}
},
"required": [
"id"
],
"type": "object"
}
},
"description": "Filtering terms are the main means to select subsets of records from a Beacon response. While the name implies the application to a generated response, in practice implementations may apply them at the query stage. Note: In the processing of Beacon v2.0 requests multiple filters are assumed to be chained by the logical AND operator.",
"items": {
"$ref": "#/definitions/FilteringTerm"
},
"title": "Filtering Term Element",
"type": "array"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 86d8c3bebb92dc892e2560022884e1ddea491821 | 2022-02-22T13:58:39 | framework/json/configuration/examples/entryTypeDefinition-MIN-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"defaultSchema": {
"id": "bdfGenericEntryType-v2",
"name": "Beacon v2 default schema for a basic element.",
"referenceToSchemaDefinition": "https://raw.githubusercontent.com/ga4gh-beacon/specification-v2-default-schemas/master/default_dataset_schema.yaml"
},
"id": "individual",
"name": "Individual entry",
"ontologyTermForThisType": {
"id": "DUO:0000004",
"label": "General Research Use"
},
"partOfSpecification": "Beacon v2"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | af5cda939ff4e14fef57becbd05ccc3da6adc8a5 | 2022-06-20T09:22:16 | models/json/beacon-v2-default-model/genomicVariations/requestParametersComponents.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"definitions": {
"AlternateBases": {
"description": "Alternate bases for this variant (starting from `start`). * Accepted values: `[ACGTN]*` * N is a wildcard, that denotes the position of any base,\n and can be used as a standalone base of any type or within a partially known\n sequence. As example, a query of `ANNT` the Ns can take take any form of [ACGT]\n and will match `ANNT`, `ACNT`, `ACCT`, `ACGT` ... and so forth.\n* an *empty value* is used in the case of deletions with the maximally trimmed,\n deleted sequence being indicated in `ReferenceBases`\n* Categorical variant queries, e.g. such *not* being represented through\n sequence & position, make use of the `variantType` parameter.\n* either `alternateBases` or `variantType` is required.",
"pattern": "^([ACGTUNRYSWKMBDHV\\-\\.]*)$",
"type": "string"
},
"Assembly": {
"description": "Genomic assembly accession and version as RefSqeq assembly accession (e.g. \"GCF_000001405.39\") or a versioned assembly name or synonym such as UCSC Genome Browser assembly (e.g. \"hg38\") or Genome Reference Consortium Human (e.g. \"GRCh38.p13\") names.",
"example": [
"GCF_000001405.39",
"hg38",
"GRCh38.p13"
],
"type": "string"
},
"RefSeqId": {
"description": "Reference sequence id for genomic reference sequence in which variant coordinates are given, e.g. \"NC_000009\" for human chromosome 9. Preferably the RefSeqId, alternatively, names, synonymous or aliases e.g. \"Chr9\" could be used.",
"example": [
"NC_000009",
"Chr9",
"NC_012920.1"
],
"type": "string"
},
"ReferenceBases": {
"description": "Reference bases for this variant (starting from `start`). * Accepted values: `[ACGTN]*` * N is a wildcard, that denotes the position of any base,\n and can be used as a standalone base of any type or within a partially known\n sequence. As example, a query of `ANNT` the Ns can take take any form of [ACGT]\n and will match `ANNT`, `ACNT`, `ACCT`, `ACGT` ... and so forth.\n* an *empty value* is used in the case of insertions with the maximally trimmed, inserted\n sequence being indicated in `AlternateBases`",
"pattern": "^([ACGTUNRYSWKMBDHV\\-\\.]*)$",
"type": "string"
}
},
"description": "Component definitions used in 'requestParameters.json'. The purpose of this file is to separate components from actual parameters to avoid confusion."
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 030747a0ef492bd79dc53d3eaf9f6c16ceae236a | 2022-02-22T13:50:28 | framework/json/configuration/examples/beaconConfiguration-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"entryTypes": {
"dataset": {
"aCollectionOf": [
{
"id": "exampleEntry",
"name": "Example entries"
}
],
"additionallySupportedSchemas": [],
"defaultSchema": {
"id": "datasetDefaultSchema",
"name": "Default schema for datasets",
"referenceToSchemaDefinition": "./datasets/defaultSchema.json",
"schemaVersion": "v.2"
},
"description": "A Dataset is a collection of records, like rows in a database or cards in a cardholder.",
"endpoint": "/datasets",
"filteringTermsReference": "./datasets/filteringTerms.json",
"id": "dataset",
"name": "Dataset",
"nonFilteredQueriesAllowed": true,
"ontologyTermForThisType": {
"id": "NCIT:C47824",
"label": "Data set"
},
"partOfSpecification": "Beacon v2.0"
},
"exampleEntry": {
"additionallySupportedSchemas": [],
"defaultSchema": {
"id": "ExampleEntryTypeDefaultschema",
"name": "Default schema for an example entries",
"referenceToSchemaDefinition": "./exampleEntry/defaultSchema.json",
"schemaVersion": "v.2"
},
"description": "A generic entry type to allow testing and playing with the specification.",
"endpoint": "./exampleEntries",
"filteringTermsReference": "./exampleEntry/filteringTerms.json",
"id": "exampleEntry",
"name": "Example Entry",
"nonFilteredQueriesAllowed": false,
"ontologyTermForThisType": {
"id": "NCIT:C20181",
"label": "Conceptual Entity"
},
"partOfSpecification": "Beacon v2.0"
}
},
"maturityAttributes": {
"productionStatus": "DEV"
},
"securityAttributes": {
"defaultGranularity": "boolean",
"securityLevels": [
"PUBLIC",
"REGISTERED",
"CONTROLLED"
]
}
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 030747a0ef492bd79dc53d3eaf9f6c16ceae236a | 2022-02-22T13:50:28 | framework/json/common/examples/ontologizedElement-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "Non-mandatory, longer textual description for the element.",
"id": "OEex1",
"name": "Element with a description and associated ontology term.",
"ontologyTermForThisType": {
"id": "DUO:0000004",
"label": "General Research Use"
}
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 60904b990df006b581ad41b9562360edb97402c4 | 2022-03-23T10:10:35 | models/json/beacon-v2-default-model/genomicVariations/examples/genomicVariant-MIN-VRS-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"variantInternalId": "GRCh37-1-55505652-G-A",
"variation": {
"location": {
"interval": {
"end": {
"type": "Number",
"value": 5505653
},
"start": {
"type": "Number",
"value": 5505652
},
"type": "SequenceInterval"
},
"sequenceId": "refseq:NC_000001.10",
"type": "SequenceLocation"
},
"state": {
"sequence": "A",
"type": "SequenceState"
},
"type": "Allele"
}
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 89ed443fecde703f259d5ec169ceeede37db72f9 | 2022-03-09T07:58:30 | models/json/beacon-v2-default-model/common/age.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "Age value definition. Provenance: GA4GH Phenopackets v2 `Age`",
"properties": {
"iso8601duration": {
"description": "Represents age as a ISO8601 duration (e.g., P40Y10M05D).",
"example": "P32Y6M1D",
"type": "string"
}
},
"title": "Age",
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | bc8f02a6a388140c854f3e17da3ccb779f2cbc0b | 2022-08-22T09:50:37 | framework/json/requests/beaconRequestBody.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "Schema for the Beacon request. It is named `RequestBody` to keep the same nomenclature used by OpenAPI v3, but it actually contains the definition of the whole HTTP POST request payload.",
"properties": {
"$schema": {
"$ref": "../common/beaconCommonComponents.json#/definitions/$schema"
},
"meta": {
"$ref": "./beaconRequestMeta.json",
"description": "Information relevant for building the response."
},
"query": {
"description": "Parameters to limit the list of returned results.",
"properties": {
"filters": {
"$ref": "./filteringTerms.json",
"description": "Ontology based filters. Using CURIE syntax is encouraged."
},
"includeResultsetResponses": {
"$ref": "../common/beaconCommonComponents.json#/definitions/IncludeResultsetResponses"
},
"pagination": {
"$ref": "../common/beaconCommonComponents.json#/definitions/Pagination",
"description": "Pagination parameters applied to response documents, in case of record level granularity."
},
"requestParameters": {
"$ref": "./requestParameters.json",
"description": "Parameters used for the entry type specific query elements."
},
"requestedGranularity": {
"$ref": "../common/beaconCommonComponents.json#/definitions/Granularity",
"description": "Requested granularity for the response. Beacons do not have to respond with the requested granularity, e.g. may respond with count results although record level granularity had been requested but indicate the granularity of the response in the response's metadata."
},
"testMode": {
"$ref": "../common/beaconCommonComponents.json#/definitions/TestMode",
"description": "Used for indicating that a request or response is done in a test context."
}
},
"type": "object"
}
},
"required": [
"meta"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | c8eae7c9c560d888bdbe111ab8a6d5da8af12d90 | 2022-08-09T16:00:21 | framework/json/responses/beaconFilteringTermsResponse.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"description": "The filtering terms response provides information about available individual filters for a beacon's entry types as well as optional information about the ontologies the filters belong to.",
"properties": {
"meta": {
"$ref": "./sections/beaconInformationalResponseMeta.json",
"description": "Information about the response that could be relevant for the Beacon client in order to interpret the results."
},
"response": {
"$ref": "./sections/beaconFilteringTermsResults.json",
"description": "A list of available filtering terms and resources they are defined in."
}
},
"required": [
"meta",
"response"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 030747a0ef492bd79dc53d3eaf9f6c16ceae236a | 2022-02-22T13:50:28 | framework/json/responses/examples-fullDocuments/beaconInfo-MIN-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"meta": {
"apiVersion": "string",
"beaconId": "string",
"returnedSchemas": [
{
"entityType": "info",
"schema": "beacon-info-v2.0.0"
}
]
},
"response": {
"apiVersion": "v0.3",
"environment": "dev",
"id": "org.ga4gh.beacon",
"name": "string",
"organization": {
"id": "string",
"name": "string"
}
}
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 89ed443fecde703f259d5ec169ceeede37db72f9 | 2022-03-09T07:58:30 | models/json/beacon-v2-default-model/datasets/examples/dataset-Max-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"createDateTime": "2017-01-17T20:33:40Z",
"dataUseConditions": {
"duoDataUse": [
{
"id": "DUO:0000007",
"label": "disease specific research",
"modifiers": [
{
"id": "EFO:0001645",
"label": "coronary artery disease"
}
],
"version": "17-07-2016"
}
]
},
"description": "This dataset provides examples of the actual data in this Beacon instance.",
"externalUrl": "http://example.org/wiki/Main_Page",
"id": "ds01010101",
"name": "Dataset with synthetic data",
"updateDateTime": "2017-01-17T20:33:40Z",
"version": "v1.1"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 3e6093cf1b20ac74bc021c315511094f930be1ef | 2022-02-22T11:21:39 | framework/json/responses/sections/beaconReceivedRequestSummary.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "Section of the response that summarize the request received as it has been interpreted by teh Beacon server. Although it is not expected to differ from the request received, in case of unexpected results or formats, this summary could help to determine the source of confusion or errors. The required properties include those that every request should have implicitly or explicitly. The request summary is making them explicit.",
"properties": {
"apiVersion": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/ApiVersion",
"description": "API version expected by the client to be supported by the server and used in the response format."
},
"filters": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/Filters",
"description": "Ontology based filters. CURIE syntax is encouraged to be used."
},
"includeResultsetResponses": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/IncludeResultsetResponses"
},
"pagination": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/Pagination",
"description": "Pagination to apply on the results."
},
"requestParameters": {
"$ref": "../../requests/requestParameters.json",
"description": "Dictionary of request parameters received in the RequestBody"
},
"requestedGranularity": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/Granularity",
"description": "Requested granularity. Targeted Beacon could respond or not with the requested granularity. E.g. record level granularity could be requested, but the Beacon could respond only with boolean or count results."
},
"requestedSchemas": {
"$comment": "TO DO: Add the format attribute as a uri.\n2. minItems:0 is used to confirm that an empty array is acceptable here.",
"$ref": "../../common/beaconCommonComponents.json#/definitions/ListOfSchemas",
"description": "Set of schemas to be used in the response to a request.",
"minItems": 0
},
"testMode": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/TestMode",
"description": "Used for indicating that a request was received in a test context. Purposed for compliance testing."
}
},
"required": [
"apiVersion",
"requestedSchemas",
"pagination",
"requestedGranularity"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 3e6093cf1b20ac74bc021c315511094f930be1ef | 2022-02-22T11:21:39 | framework/json/common/examples/beaconCommonComponents-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"apiVersion": "v2.0",
"beaconError": {
"errorCode": 404,
"errorMessage": "the provided parameters are incomplete. 'xyz' is missing."
},
"beaconId": "org.example.beacon.v2",
"exists": true,
"filters": [
"BTO:0000199",
"PATO:0000383"
],
"handover": {
"handoverType": {
"id": "EFO:0004157",
"label": "BAM format"
},
"note": "This handover link provides access to a summarized VCF.",
"url": "https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0"
},
"handoverType": {
"id": "EFO:0004157",
"label": "BAM format"
},
"includeResultsetResponses": "HIT",
"info": {},
"listOfHandovers": [
{
"handoverType": {
"id": "EFO:0004157",
"label": "BAM format"
},
"note": "This handover link provides access to a summarized VCF.",
"url": "https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0"
},
{
"handoverType": {
"id": "EFO:0004157",
"label": "BAM format"
},
"note": "This handover link provides access to a summarized VCF.",
"url": "https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0"
}
],
"listOfSchemas": [
{
"entityType": "EntryTypeA",
"schema": "entry-typeA-schema-v0.1"
},
{
"entityType": "EntryTypeB",
"schema": "entry-typeB-schema-v1.0"
}
],
"numTotalResults": 123,
"pagination": {
"limit": 10,
"skip": 0
},
"schemasPerEntity": {
"entityType": "Individual",
"schema": "ga4gh-phenopacket-individual-v0.1"
}
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 030747a0ef492bd79dc53d3eaf9f6c16ceae236a | 2022-02-22T13:50:28 | framework/json/common/examples/elementWithDescription-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "A longer textual description for the element.",
"id": "EWDex1",
"name": "Element with description one"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 3e6093cf1b20ac74bc021c315511094f930be1ef | 2022-02-22T11:21:39 | framework/json/responses/beaconFilteringTermsResponse.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"description": "List of filtering terms response.",
"properties": {
"meta": {
"$ref": "./sections/beaconInformationalResponseMeta.json",
"description": "Information about the response that could be relevant for the Beacon client in order to interpret the results."
},
"response": {
"$ref": "./sections/beaconFilteringTermsResults.json",
"description": "Actual list of filtering terms."
}
},
"required": [
"meta",
"response"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 030747a0ef492bd79dc53d3eaf9f6c16ceae236a | 2022-02-22T13:50:28 | framework/json/requests/requestParameters.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": {
"type": "object"
},
"description": "The schema below is suited for a dictionary 'key':'object', which is the case of the parameter definitions.",
"properties": {
"$schema": {
"description": "Added here to allow proper validation of the documents.",
"type": "string"
}
},
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 86d8c3bebb92dc892e2560022884e1ddea491821 | 2022-02-22T13:58:39 | framework/json/requests/examples-sections/requestParameters-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"exampleEntry": {
"description": "All the required fields to query any kind of variant (e.g. SNP, DUP,\netc.).",
"properties": {
"id": {
"description": "Id of the entry to display.",
"type": "string"
}
},
"type": "object"
}
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 3e6093cf1b20ac74bc021c315511094f930be1ef | 2022-02-22T11:21:39 | framework/json/responses/sections/beaconFilteringTermsResults.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"definitions": {
"FilteringTerm": {
"description": "Entities can be filtered using this term.",
"properties": {
"id": {
"description": "The field id in the case of numeric or alphanumeric fields, or the term id in the case of ontology or custom terms. CURIE syntax in the case of an ontology term.",
"example": "HP:0008773",
"type": "string"
},
"label": {
"description": "This would be the \"preferred Label\" in the case of an ontology term.",
"example": "Aplasia/Hypoplasia of the middle ear",
"type": "string"
},
"type": {
"description": "Either \"custom\", \"alphanumeric\" or ontology/terminology full name.",
"example": "Human Phenotype Ontology",
"type": "string"
}
},
"required": [
"type",
"id"
],
"type": "object"
},
"Resource": {
"description": "Description of an ontology resource defined externally to this beacon implementation, such as MeSH or EFO, based on the phenopackets resource object (https://phenopacket-schema.readthedocs.io/en/latest/resource.html)",
"properties": {
"id": {
"description": "OBO ID representing the resource",
"example": "hp",
"type": "string"
},
"iriPrefix": {
"description": "The full Internationalized Resource Identifier (IRI) prefix",
"example": "http://purl.obolibrary.org/obo/HP_",
"type": "string"
},
"name": {
"description": "The name of the ontology referred to by the id element",
"example": "Human Phenotype Ontology",
"type": "string"
},
"nameSpacePrefix": {
"description": "The prefix used in the CURIE of an OntologyClass",
"example": "HP",
"type": "string"
},
"url": {
"description": "Uniform Resource Locator of the resource",
"example": "http://purl.obolibrary.org/obo/hp.owl",
"type": "string"
},
"version": {
"description": "The version of the resource or ontology used to make the annotation",
"example": "17-06-2019",
"type": "string"
}
},
"required": [
"id"
],
"type": "object"
}
},
"description": "Filtering terms and ontology resources utilised in this Beacon.",
"properties": {
"filteringTerms": {
"items": {
"$ref": "#/definitions/FilteringTerm"
},
"type": "array"
},
"resources": {
"description": "Ontology resources defined externally to this beacon implementation",
"items": {
"$ref": "#/definitions/Resource"
},
"type": "array"
}
},
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 5637b6343d049e2829d3369edf806398027e6b33 | 2022-04-06T12:44:16 | framework/json/configuration/beaconConfigurationSchema.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"definitions": {
"EntryTypes": {
"additionalProperties": {
"$ref": "./entryTypeDefinition.json",
"type": "object"
},
"description": "This is a dictionary of the entry types implemented in this Beacon instance.",
"minProperties": 1,
"type": "object"
}
},
"description": "Files complaint with this schema are the configuration ones. The details returned in `service-info` are mirroring the ones in this configuration file.",
"properties": {
"$schema": {
"$ref": "../common/beaconCommonComponents.json#/definitions/$schema"
},
"entryTypes": {
"$ref": "#/definitions/EntryTypes"
},
"maturityAttributes": {
"description": "Declares the level of maturity of the Beacon instance.",
"properties": {
"productionStatus": {
"description": "`DEV`= 'Service potentially unstable, not real data', which availability and data should not be used in production setups. `TEST`= 'Service stable, not real data'. 'PROD'= 'Service stable, actual data'.",
"enum": [
"DEV",
"TEST",
"PROD"
],
"type": "string"
}
},
"type": "object"
},
"securityAttributes": {
"description": "Configuration of the security aspects of the Beacon. By default, a Beacon that does not declare the configuration settings would return `boolean` (true/false) responses, and only if the user is authenticated and explicitly authorized to access the Beacon resources. Although this is the safest set of settings, it is not recommended unless the Beacon shares very sensitive information. Non sensitive Beacons should preferably opt for a `record` and `PUBLIC` combination.",
"properties": {
"defaultGranularity": {
"$ref": "../common/beaconCommonComponents.json#/definitions/Granularity",
"description": "Default granularity. Some responses could return higher detail, but this would be the granularity by default."
},
"securityLevels": {
"description": "All access levels supported by the Beacon. Any combination is valid, as every option would apply to different parts of the Beacon.",
"items": {
"default": [
"CONTROLLED"
],
"enum": [
"PUBLIC",
"REGISTERED",
"CONTROLLED"
]
},
"type": "array"
}
},
"type": "object"
}
},
"required": [
"$schema",
"maturityAttributes",
"entryTypes"
],
"title": "Beacon Configuration",
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 5468efe2aeea4398e89c1321ae060ceba835571e | 2023-06-04T13:51:19 | framework/json/responses/sections/beaconFilteringTermsResults.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"definitions": {
"FilteringTerm": {
"description": "Entities can be filtered using this term.",
"properties": {
"id": {
"description": "The field id in the case of numeric or alphanumeric fields, or the term id in the case of ontology or custom terms. CURIE syntax in the case of an ontology term.",
"examples": [
"NCIT:C8936",
"HP:0008773"
],
"type": "string"
},
"label": {
"description": "This would be the \"preferred Label\" in the case of an ontology term.",
"examples": [
"B Lymphoblastic Leukemia/Lymphoma",
"Aplasia/Hypoplasia of the middle ear"
],
"type": "string"
},
"type": {
"description": "Either \"custom\", \"alphanumeric\" or ontology/terminology full name. TODO: An ontology ... with a registered prefix does not need a full name so one may better use CURIE to indicate that the resource can be retrieved from the id. This also will allow to provide an enum here.",
"examples": [
"Human Phenotype Ontology",
"alphanumeric"
],
"type": "string"
}
},
"required": [
"type",
"id"
],
"type": "object"
},
"Resource": {
"description": "Description of an ontology resource defined externally to this beacon implementation, such as MeSH or EFO, based on the phenopackets resource object (https://phenopacket-schema.readthedocs.io/en/latest/resource.html)",
"properties": {
"id": {
"description": "Preferably OBO ID representing the resource; alternatively a URI pointing towards the definitions may be used if not in OBO.",
"examples": [
"hp"
],
"type": "string"
},
"iriPrefix": {
"description": "The full Internationalized Resource Identifier (IRI) prefix",
"examples": [
"https://purl.obolibrary.org/obo/HP_"
],
"type": "string"
},
"name": {
"description": "The name of the ontology referred to by the id element",
"examples": [
"Human Phenotype Ontology"
],
"type": "string"
},
"nameSpacePrefix": {
"description": "The prefix used in the CURIE of an OntologyClass",
"examples": [
"HP"
],
"type": "string"
},
"url": {
"description": "Uniform Resource Locator of the resource",
"examples": [
"https://purl.obolibrary.org/obo/hp.owl"
],
"type": "string"
},
"version": {
"description": "The version of the resource or ontology used to make the annotation",
"examples": [
"17-06-2019"
],
"type": "string"
}
},
"required": [
"id"
],
"type": "object"
}
},
"description": "Filtering terms and ontology resources utilised in this Beacon.",
"properties": {
"filteringTerms": {
"items": {
"$ref": "#/definitions/FilteringTerm"
},
"type": "array"
},
"resources": {
"items": {
"$ref": "#/definitions/Resource"
},
"type": "array"
}
},
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 1447418ae20062d48c6644b705a4e0c31b8355af | 2024-03-20T15:28:22 | framework/json/responses/sections/beaconFilteringTermsResults.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"definitions": {
"FilteringTerm": {
"description": "Entities can be filtered using this term.",
"properties": {
"id": {
"description": "The field id in the case of numeric or alphanumeric fields, or the term id in the case of ontology or custom terms. CURIE syntax in the case of an ontology term.",
"examples": [
"NCIT:C8936",
"HP:0008773"
],
"type": "string"
},
"label": {
"description": "This would be the \"preferred Label\" in the case of an ontology term.",
"examples": [
"B Lymphoblastic Leukemia/Lymphoma",
"Aplasia/Hypoplasia of the middle ear"
],
"type": "string"
},
"scopes": {
"description": "Entry types affected by this filter.",
"examples": [
[
"individual",
"biosample",
"analysis",
"run",
"genomicVariation"
],
[
"biosample"
]
],
"items": {
"type": "string"
},
"type": "array"
},
"type": {
"description": "Either \"custom\", \"alphanumeric\" or ontology/terminology full name. TODO: An ontology ... with a registered prefix does not need a full name so one may better use CURIE to indicate that the resource can be retrieved from the id. This also will allow to provide an enum here.",
"examples": [
"Human Phenotype Ontology",
"alphanumeric"
],
"type": "string"
}
},
"required": [
"type",
"id"
],
"type": "object"
},
"Resource": {
"description": "Description of an ontology resource defined externally to this beacon implementation, such as MeSH or EFO, based on the phenopackets resource object (https://phenopacket-schema.readthedocs.io/en/latest/resource.html)",
"properties": {
"id": {
"description": "Preferably OBO ID representing the resource; alternatively a URI pointing towards the definitions may be used if not in OBO.",
"examples": [
"hp"
],
"type": "string"
},
"iriPrefix": {
"description": "The full Internationalized Resource Identifier (IRI) prefix",
"examples": [
"http://purl.obolibrary.org/obo/HP_"
],
"type": "string"
},
"name": {
"description": "The name of the ontology referred to by the id element",
"examples": [
"Human Phenotype Ontology"
],
"type": "string"
},
"nameSpacePrefix": {
"description": "The prefix used in the CURIE of an OntologyClass",
"examples": [
"HP"
],
"type": "string"
},
"url": {
"description": "Uniform Resource Locator of the resource",
"examples": [
"http://purl.obolibrary.org/obo/hp.owl"
],
"type": "string"
},
"version": {
"description": "The version of the resource or ontology used to make the annotation",
"examples": [
"17-06-2019"
],
"type": "string"
}
},
"required": [
"id"
],
"type": "object"
}
},
"description": "Filtering terms and ontology resources utilised in this Beacon.",
"properties": {
"filteringTerms": {
"items": {
"$ref": "#/definitions/FilteringTerm"
},
"type": "array"
},
"resources": {
"items": {
"$ref": "#/definitions/Resource"
},
"type": "array"
}
},
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 86d8c3bebb92dc892e2560022884e1ddea491821 | 2022-02-22T13:58:39 | framework/json/responses/sections/beaconCountResponseSection.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "Total number of results section.",
"properties": {
"exists": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/Exists",
"description": "Indicator of whether any entry was observed. This should be non-null, unless there was an error, in which case an error response is expected instead of this one."
},
"numTotalResults": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/NumTotalResults",
"description": "Total number of results."
}
},
"required": [
"exists",
"numTotalResults"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 89ed443fecde703f259d5ec169ceeede37db72f9 | 2022-03-09T07:58:30 | models/json/beacon-v2-default-model/common/commonDefinitions.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"definitions": {
"Ethnicity": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-unity-testing/main/framework/json/common/ontologyTerm.json",
"description": "Ethnic background of the individual. Value from NCIT Race (NCIT:C17049) ontology term descendants, e.g. NCIT:C126531 (Latin American). A geographic ancestral origin category that is assigned to a population group based mainly on physical characteristics that are thought to be distinct and inherent. [ NCI ] ",
"examples": [
{
"id": "NCIT:C42331",
"label": "African"
},
{
"id": "NCIT:C41260",
"label": "Asian"
},
{
"id": "NCIT:C126535",
"label": "Australian"
},
{
"id": "NCIT:C43851",
"label": "European"
},
{
"id": "NCIT:C77812",
"label": "North American"
},
{
"id": "NCIT:C126531",
"label": "Latin American"
},
{
"id": "NCIT:C104495",
"label": "Other race"
}
]
},
"GeographicLocation": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-unity-testing/main/framework/json/common/ontologyTerm.json",
"description": "Individual's country or region of origin (birthplace or residence place regardless of ethnic origin). Value from GAZ Geographic Location ontology (GAZ:00000448), e.g. GAZ:00002459 (United States of America).",
"examples": [
{
"id": "GAZ:00002955",
"label": "Slovenia"
},
{
"id": "GAZ:00002459",
"label": "United States of America"
},
{
"id": "GAZ:00316959",
"label": "Municipality of El Masnou"
},
{
"id": "GAZ:00000460",
"label": "Eurasia"
}
]
},
"SeverityLevel": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-unity-testing/main/framework/json/common/ontologyTerm.json",
"description": "Level/severity ontology when and as applicable to phenotype observed. Value from Human Phenotype Ontology (HP:0012824), e.g \"mild\". The intensity or degree of a manifestation. [ HPO:probinson ] ",
"examples": [
{
"id": "HP:0012825",
"label": "Severe"
},
{
"id": "HP:0012829",
"label": "Profound"
},
{
"id": "HP:0012826",
"label": "Moderate"
},
{
"id": "HP:0012825",
"label": "Mild"
},
{
"id": "HP:0012827",
"label": "Bordeline"
}
]
},
"Sex": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-unity-testing/main/framework/json/common/ontologyTerm.json",
"description": "Sex of the individual. Value from NCIT General Qualifier (NCIT:C27993): 'unknown' (not assessed or not available) (NCIT:C17998), 'female' (NCIT:C16576), or 'male', (NCIT:C20197).",
"examples": [
{
"id": "NCIT:C16576",
"label": "female"
},
{
"id": "NCIT:C20197",
"label": "male"
},
{
"id": "NCIT:C1799",
"label": "unknown"
}
]
},
"Unit": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-unity-testing/main/framework/json/common/ontologyTerm.json",
"description": "The kind of unit. Recommended from NCIT Unit of Category ontology term (NCIT:C42568) descendants",
"examples": [
{
"id": "NCIT:C70575",
"label": "Roentgen"
},
{
"id": "NCIT:C28252",
"label": "Kilogram"
},
{
"id": "NCIT:C28253",
"label": "Milligram"
}
]
}
},
"description": "Definitions for concepts used in several entry types, but that having only one property are not complex enough to require a full independent schema document.",
"title": "Common Definitions"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | dfbdc0b38fe322521955e22bf863f26933774d3d | 2022-03-30T15:52:26 | models/json/beacon-v2-default-model/genomicVariations/requestParameters.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"g_variant": {
"properties": {
"alternateBases": {
"$ref": "./requestParametersComponents.json#/definitions/AlternateBases"
},
"aminoacidChange": {
"description": "Aminoacid alteration of interest. Format 1 letter ",
"examples": [
"V600E",
"M734V"
],
"type": "string"
},
"assemblyId": {
"$ref": "./requestParametersComponents.json#/definitions/Assembly"
},
"end": {
"description": "Precise or bracketing the end of the variants of interest:\n* (0-based, exclusive) - see `start`\n* for bracket queries, provide 2 values (e.g. [111,222]).",
"items": {
"format": "int64",
"minimum": 1,
"type": "integer"
},
"maxItems": 2,
"minItems": 0,
"type": "array"
},
"geneId": {
"description": "Gene identifier, it is strongly suggested to use a symbol following the HGNC (https://www.genenames.org) nomenclature.",
"examples": [
"BRAF",
"SCN5A"
],
"type": "string"
},
"genomicAlleleShortForm": {
"description": "HGVSId descriptor",
"examples": [
"NM_004006.2:c.4375C>T"
],
"type": "string"
},
"mateName": {
"$ref": "./requestParametersComponents.json#/definitions/RefSeqId"
},
"referenceBases": {
"$ref": "./requestParametersComponents.json#/definitions/ReferenceBases"
},
"referenceName": {
"$ref": "./requestParametersComponents.json#/definitions/RefSeqId"
},
"start": {
"description": "Precise or fuzzy start coordinate position(s), allele locus\n(0-based, inclusive).\n* `start` only:\n - for single positions, e.g. the start of a specified sequence\n alteration where the size is given through the specified\n `alternateBases`\n - typical use are queries for SNV and small InDels\n - the use of `start` without an `end` parameter requires the use\n of `alternateBases`\n\n* `start` and `end`:\n - for searching any variant falling fully or partially within the\n range between `start` and `end` (a.k.a. \"range query\")\n - additional use of `variantType` OR `alternateBases` can limit the\n scope of the query\n - by convention, partial overlaps of variants with the indicated\n genomic range are accepted; for specific overlap requirements the\n 4-parammeter \"Bracket Queries\" should be employed\n* use of 2 values in both `start` and `end` for constructing a\n\"Bracket Query\":\n - can be used to match any contiguous genomic interval, e.g. for\n querying imprecise positions\n * identifying all structural variants starting between `start[0]`\n and `start[1]`, and ending between `end[0]` <-> `end[1]`\n * single or double sided precise matches can be achieved by\n setting `start[1]=start[0]+1` and `end[1]=end[0]+1`",
"items": {
"format": "int64",
"minimum": 0,
"type": "integer"
},
"maxItems": 2,
"minItems": 1,
"type": "array"
},
"variantMaxLength": {
"description": "Maximum length in bases of a genomic variant. This is an optional parameter without prescribed use. While a length is commonly available for structural variants such as copy number variations, it is recommended that length based queries should also be supported for variants with indicated referenceBases and alternateBases, to enable length-specific wildcard queries.",
"format": "int64",
"minimum": 1,
"type": "integer"
},
"variantMinLength": {
"description": "Minimum length in bases of a genomic variant. This is an optional parameter without prescribed use. While a length is commonly available for structural variants such as copy number variations, it is recommended that length based queries should also be supported for variants with indicated referenceBases and alternateBases, to enable length-specific wildcard queries.",
"format": "int64",
"minimum": 0,
"type": "integer"
},
"variantType": {
"description": "The `variantType` is used to query variants which are not defined\nthrough a sequence of one or more bases using the `alternateBases`\nparameter. Examples here are e.g. structural variants:\n* DUP\n - increased allelic count of material from the genomic region\n between `start` and `end` positions\n - no assumption about the placement of the additional sequences is\n being made (i.e. no _in situ_ requirement as tandem duplications)\n* DEL: deletion of sequence following `start`\n* BND: breakend, i.e. termination of the allele at position\n `start` or in the `startMin` => `startMax` interval, or fusion\n of the sequence to distant partner\nEither `alternateBases` or `variantType` is required, with the\nexception of range queries (single `start` and `end` parameters).",
"type": "string"
}
},
"type": "object"
}
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 030747a0ef492bd79dc53d3eaf9f6c16ceae236a | 2022-02-22T13:50:28 | framework/json/configuration/examples/beaconConfigurationFilteringTerms-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"filteringTerms": [
{
"ftType": "alphanumeric",
"id": "age",
"scope": "individual"
},
{
"ftType": "ontologyTerm",
"id": "HP:0002664",
"label": "Neoplasm",
"scope": "biosample"
},
{
"ftType": "alphanumeric",
"id": "NCIT:C100094",
"label": "HGNC gene name",
"scope": "genomicVariant"
}
]
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 89ed443fecde703f259d5ec169ceeede37db72f9 | 2022-03-09T07:58:30 | models/json/beacon-v2-default-model/cohorts/examples/cohorts-MIN-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"cohortId": "cohort0001",
"cohortName": "GCAT Genomes for Life",
"cohortType": "study-defined"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 8e09eabe19cfa57526eefd1765154ec2c985eede | 2022-10-11T11:03:58 | framework/json/responses/sections/beaconResultsets.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"definitions": {
"ResultsetInstance": {
"additionalProperties": true,
"properties": {
"exists": {
"type": "boolean"
},
"id": {
"description": "id of the resultset",
"example": "datasetA",
"type": "string"
},
"info": {
"description": "Additional details that could be of interest about the Resultset. Provided to clearly enclose any attribute that is not part of the Beacon specification.",
"type": "object"
},
"results": {
"items": {
"type": "object"
},
"minItems": 0,
"type": "array"
},
"resultsCount": {
"description": "Number of results in this Resultset.",
"type": "integer"
},
"resultsHandovers": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/ListOfHandovers",
"description": "List of handovers that apply to this resultset, not to the whole Beacon or to a result in particular."
},
"setType": {
"default": "dataset",
"description": "Entry type of resultSet. It SHOULD MATCH an entry type declared as collection in the Beacon configuration.",
"type": "string"
}
},
"required": [
"id",
"setType",
"exists",
"resultsCount",
"results"
]
}
},
"description": "Sets of results to be returned as query response.",
"properties": {
"$schema": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/$schema"
},
"resultSets": {
"items": {
"$ref": "#/definitions/ResultsetInstance"
},
"minItems": 0,
"type": "array"
}
},
"required": [
"resultSets"
],
"title": "Beacon ResultSet",
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 86d8c3bebb92dc892e2560022884e1ddea491821 | 2022-02-22T13:58:39 | framework/json/responses/beaconFilteringTermsResponse.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"description": "List of filtering terms response.",
"properties": {
"meta": {
"$ref": "./sections/beaconInformationalResponseMeta.json",
"description": "Information about the response that could be relevant for the Beacon client in order to interpret the results."
},
"response": {
"$ref": "./sections/beaconFilteringTermsResults.json",
"description": "Actual list of filtering terms."
}
},
"required": [
"meta",
"response"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 89ed443fecde703f259d5ec169ceeede37db72f9 | 2022-03-09T07:58:30 | models/json/beacon-v2-default-model/cohorts/filteringTerms.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"filteringTerms": [
{
"ftType": "ontologyTerm",
"id": "DUO:0000006",
"label": "health or medical or biomedical research",
"version": "2021-02-23"
}
]
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 3e6093cf1b20ac74bc021c315511094f930be1ef | 2022-02-22T11:21:39 | framework/json/responses/examples-fullDocuments/beaconCountResponse-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"beaconHandovers": [
{
"handoverType": {
"id": "EFO:0004157",
"label": "BAM format"
},
"note": "This handover link provides access to a summarized VCF.",
"url": "https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0"
},
{
"handoverType": {
"id": "EFO:0004157",
"label": "BAM format"
},
"note": "This handover link provides access to a summarized VCF.",
"url": "https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0"
}
],
"info": {
"someInterestingStuff": "this is the interesting stuff"
},
"meta": {
"apiVersion": "v2.0",
"beaconId": "org.example.beacon.v2",
"receivedRequestSummary": {
"apiVersion": "2.0",
"pagination": {
"limit": 10,
"skip": 0
},
"requestedSchemas": [
{
"entityType": "EntryTypeB",
"schema": "entry-typeB-schema-v1.0"
}
]
},
"returnedSchemas": [
{
"entityType": "EntryTypeB",
"schema": "entry-typeB-schema-v1.0"
}
]
},
"responseSummary": {
"exists": true,
"numTotalResults": 25355
}
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 030747a0ef492bd79dc53d3eaf9f6c16ceae236a | 2022-02-22T13:50:28 | framework/json/responses/examples-fullDocuments/beaconResultsetResponse-MIN-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"meta": {
"apiVersion": "v2.0",
"beaconId": "org.example.beacon.v2",
"receivedRequestSummary": {
"apiVersion": "2.0",
"pagination": {
"limit": 10,
"skip": 0
},
"requestedSchemas": [
{
"entityType": "EntryTypeB",
"schema": "entry-typeB-schema-v1.0"
}
]
},
"returnedSchemas": [
{
"entityType": "EntryTypeB",
"schema": "entry-typeB-schema-v1.0"
}
]
},
"responseSummary": {
"exists": true
},
"resultSets": []
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 86d8c3bebb92dc892e2560022884e1ddea491821 | 2022-02-22T13:58:39 | framework/json/responses/beaconConfigurationResponse.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"description": "Information about the Beacon. Aimed to Beacon clients like web pages or Beacon networks.",
"properties": {
"meta": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-unity/main/framework/json/responses/sections/beaconInformationalResponseMeta.json",
"description": "Information about the response that could be relevant for the Beacon client in order to interpret the results."
},
"response": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-unity/main/framework/json/configuration/beaconConfigurationSchema.json",
"description": "Returning the Beacon configuration."
}
},
"required": [
"meta",
"response"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 3e6093cf1b20ac74bc021c315511094f930be1ef | 2022-02-22T11:21:39 | framework/json/responses/ga4gh-service-info-1-0-0-schema.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"definitions": {
"ServiceType": {
"description": "Type of a GA4GH service",
"properties": {
"artifact": {
"description": "Name of the API or GA4GH specification implemented. Official GA4GH types should be assigned as part of standards approval process. Custom artifacts are supported.",
"example": "beacon",
"type": "string"
},
"group": {
"description": "Namespace in reverse domain name format. Use `org.ga4gh` for implementations compliant with official GA4GH specifications. For services with custom APIs not standardized by GA4GH, or implementations diverging from official GA4GH specifications, use a different namespace (e.g. your organization's reverse domain name).",
"example": "org.ga4gh",
"type": "string"
},
"version": {
"description": "Version of the API or specification. GA4GH specifications use semantic versioning.",
"example": "1.0.0",
"type": "string"
}
},
"required": [
"group",
"artifact",
"version"
],
"type": "object"
}
},
"description": "A way for a service to describe basic metadata concerning a service alongside a set of capabilities and/or limitations of the service. More information on [GitHub](https://github.com/ga4gh-discovery/ga4gh-service-info/).",
"properties": {
"contactUrl": {
"description": "URL of the contact for the provider of this service, e.g. a link to a contact form (RFC 3986 format), or an email (RFC 2368 format).",
"example": "mailto:[email protected]",
"format": "uri",
"type": "string"
},
"createdAt": {
"description": "Timestamp describing when the service was first deployed and available (RFC 3339 format)",
"example": "2019-06-04T12:58:19Z",
"format": "date-time",
"type": "string"
},
"description": {
"description": "Description of the service. Should be human readable and provide information about the service.",
"example": "This service provides...",
"type": "string"
},
"documentationUrl": {
"description": "URL of the documentation of this service (RFC 3986 format). This should help someone learn how to use your service, including any specifics required to access data, e.g. authentication.",
"example": "https://docs.myservice.example.com",
"format": "uri",
"type": "string"
},
"environment": {
"description": "Environment the service is running in. Use this to distinguish between production, development and testing/staging deployments. Suggested values are prod, test, dev, staging. However this is advised and not enforced.",
"example": "test",
"type": "string"
},
"id": {
"description": "Unique ID of this service. Reverse domain name notation is recommended, though not required. The identifier should attempt to be globally unique so it can be used in downstream aggregator services e.g. Service Registry.",
"example": "org.ga4gh.myservice",
"type": "string"
},
"name": {
"description": "Name of this service. Should be human readable.",
"example": "My project",
"type": "string"
},
"organization": {
"description": "Organization providing the service",
"properties": {
"name": {
"description": "Name of the organization responsible for the service",
"example": "My organization",
"type": "string"
},
"url": {
"description": "URL of the website of the organization (RFC 3986 format)",
"example": "https://example.com",
"format": "uri",
"type": "string"
}
},
"required": [
"name",
"url"
],
"type": "object"
},
"type": {
"$ref": "#/definitions/ServiceType"
},
"updatedAt": {
"description": "Timestamp describing when the service was last updated (RFC 3339 format)",
"example": "2019-06-04T12:58:19Z",
"format": "date-time",
"type": "string"
},
"version": {
"description": "Version of the service being described. Semantic versioning is recommended, but other identifiers, such as dates or commit hashes, are also allowed. The version should be changed whenever the service is updated.",
"example": "1.0.0",
"type": "string"
}
},
"required": [
"id",
"name",
"type",
"organization",
"version"
],
"title": "GA4GH service-info API specification",
"type": "object",
"version": "1.0.0"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 2a2b786e4a1845ea23d71dfe8125957b6f3d742f | 2022-06-20T13:19:32 | framework/json/responses/beaconConfigurationResponse.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"description": "Information about the Beacon. Aimed to Beacon clients like web pages or Beacon networks.",
"properties": {
"meta": {
"$ref": "./sections/beaconInformationalResponseMeta.json",
"description": "Information about the response that could be relevant for the Beacon client in order to interpret the results."
},
"response": {
"$ref": "../configuration/beaconConfigurationSchema.json",
"description": "Returning the Beacon configuration."
}
},
"required": [
"meta",
"response"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 030747a0ef492bd79dc53d3eaf9f6c16ceae236a | 2022-02-22T13:50:28 | framework/json/responses/examples-sections/beaconReceivedRequestSummary-MIN-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"apiVersion": "v2.0",
"pagination": {},
"requestedGranularity": "boolean",
"requestedSchemas": []
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 030747a0ef492bd79dc53d3eaf9f6c16ceae236a | 2022-02-22T13:50:28 | framework/json/common/examples/ontologyTerm-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"id": "DUO:0000004",
"label": "General Research Use"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 8de7dd4a5b930eac822073d21939eb4e92a06335 | 2022-07-22T14:00:24 | bin/adhoc/ontologyTerm.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"properties": {
"id": {
"$ref": "./beaconCommonComponents.json#/definitions/CURIE"
},
"label": {
"description": "The text that describes the term. By default it could be the preferred text of the term, but is it acceptable to customize it for a clearer description and understanding of the term in an specific context.",
"type": "string"
}
},
"required": [
"id"
],
"title": "Ontology Term",
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 60904b990df006b581ad41b9562360edb97402c4 | 2022-03-23T10:10:35 | models/json/beacon-v2-default-model/common/commonDefinitions.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"definitions": {
"Ethnicity": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json",
"description": "Ethnic background of the individual. Recommended is the use of a value from NCIT Race (NCIT:C17049) ontology term descendants, e.g. NCIT:C126531 (Latin American). A geographic ancestral origin category that is assigned to a population group based mainly on physical characteristics that are thought to be distinct and inherent. [ NCI ]",
"examples": [
{
"id": "NCIT:C42331",
"label": "African"
},
{
"id": "NCIT:C41260",
"label": "Asian"
},
{
"id": "NCIT:C126535",
"label": "Australian"
},
{
"id": "NCIT:C43851",
"label": "European"
},
{
"id": "NCIT:C77812",
"label": "North American"
},
{
"id": "NCIT:C126531",
"label": "Latin American"
},
{
"id": "NCIT:C104495",
"label": "Other race"
}
]
},
"GeographicLocation": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json",
"description": "Country or region of origin of the individual (birthplace or residence place regardless of ethnic origin). Value from GAZ Geographic Location ontology (GAZ:00000448), e.g. GAZ:00002459 (United States of America).",
"examples": [
{
"id": "GAZ:00002955",
"label": "Slovenia"
},
{
"id": "GAZ:00002459",
"label": "United States of America"
},
{
"id": "GAZ:00316959",
"label": "Municipality of El Masnou"
},
{
"id": "GAZ:00000460",
"label": "Eurasia"
}
]
},
"KaryotypicSex": {
"$comments": "Compares to https://github.com/phenopackets/phenopacket-schema/blob/master/docs/karyotypicsex.rst",
"default": "UNKNOWN_KARYOTYPE",
"description": "The chromosomal sex of an individual represented from a selection of options. The values correspond to the ordinal values in the Phenopackets schema where: 0 - UNKNOWN_KARYOTYPE (Untyped or inconclusive karyotyping); 1 - XX (Female); 2 - XY (Male); 3 - XO (Single X chromosome only); 4 - XXY (Two X and one Y chromosome); 5 - XXX (Three X chromosomes); 6 - XXYY (Two X chromosomes and two Y chromosomes); 7 - XXXY (Three X chromosomes and one Y chromosome); 8 - XXXX (Four X chromosomes); 9 - XYY (One X and two Y chromosomes); 10 - OTHER_KARYOTYPE (None of the above types)",
"enum": [
"UNKNOWN_KARYOTYPE",
"XX",
"XY",
"XO",
"XXY",
"XXX",
"XXYY",
"XXXY",
"XXXX",
"XYY",
"OTHER_KARYOTYPE"
],
"type": "string"
},
"SeverityLevel": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json",
"description": "Level/severity ontology when and as applicable to phenotype observed. Value from Human Phenotype Ontology (HP:0012824), e.g `mild`. The intensity or degree of a manifestation. [ HPO:probinson ] ",
"examples": [
{
"id": "HP:0012825",
"label": "Severe"
},
{
"id": "HP:0012829",
"label": "Profound"
},
{
"id": "HP:0012826",
"label": "Moderate"
},
{
"id": "HP:0012825",
"label": "Mild"
},
{
"id": "HP:0012827",
"label": "Bordeline"
}
]
},
"Sex": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json",
"description": "Sex of the individual. Recommended values from NCIT General Qualifier (NCIT:C27993): \"unknown\" (not assessed or not available) - NCIT:C17998; \"female\" - NCIT:C16576; \"male\" - NCIT:C20197",
"examples": [
{
"id": "NCIT:C16576",
"label": "female"
},
{
"id": "NCIT:C20197",
"label": "male"
},
{
"id": "NCIT:C1799",
"label": "unknown"
}
]
},
"Timestamp": {
"description": "Time in date-time ISO8601 string format.",
"examples": [
"1999-08-05T17:21:00+01:00",
"2002-09-21T02:37:00-08:00"
],
"format": "date-time",
"type": "string"
},
"Unit": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json",
"description": "The kind of unit. Recommended from NCIT Unit of Category ontology term (NCIT:C42568) descendants",
"examples": [
{
"id": "NCIT:C70575",
"label": "Roentgen"
},
{
"id": "NCIT:C28252",
"label": "Kilogram"
},
{
"id": "NCIT:C28253",
"label": "Milligram"
}
]
}
},
"description": "Definitions for concepts used in several entry types, but that having only one property are not complex enough to require a full independent schema document.",
"title": "Common Definitions"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 2c53ba10fba1bf39152e286d3a6edc756de7f6fc | 2022-04-05T15:50:47 | models/json/beacon-v2-default-model/genomicVariations/examples/genomicVariant-MIN-VRS-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"variantInternalId": "GRCh37-1-55505652-G-A",
"variation": {
"location": {
"interval": {
"end": {
"type": "Number",
"value": 5505653
},
"start": {
"type": "Number",
"value": 5505652
},
"type": "SequenceInterval"
},
"sequence_id": "refseq:NC_000001.10",
"type": "SequenceLocation"
},
"state": {
"sequence": "A",
"type": "SequenceState"
},
"type": "Allele"
}
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 9eaada7ca0410f4127d0c324880033e60024d128 | 2022-03-13T12:14:16 | models/json/beacon-v2-default-model/runs/examples/runs-MIN-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"biosampleId": "008dafdd-a3d1-4801-8c0a-8714e2b58e48",
"id": "SRR10903401",
"runDate": "2021-10-18"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | a45ccc786aba78e1e393bb4c087c1d87d9ae5306 | 2023-10-06T14:14:36 | models/json/beacon-v2-default-model/common/ageRange.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "Age range definition. Provenance: GA4GH Phenopackets v2 `AgeRange`",
"properties": {
"end": {
"$ref": "./age.json",
"description": "Represents age as an ISO8601 duration (e.g., P59Y)."
},
"start": {
"$ref": "./age.json",
"description": "Represents age as an ISO8601 duration (e.g., P18Y)."
}
},
"required": [
"end",
"start"
],
"title": "AgeRange",
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 89ed443fecde703f259d5ec169ceeede37db72f9 | 2022-03-09T07:58:30 | models/json/beacon-v2-default-model/analyses/examples/analyses-MAX-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"aligner": "bwa-0.7.8",
"analysisDate": "2021-10-17",
"biosampleId": "S0001",
"id": "analyses-example-0001",
"individualId": "P0001",
"pipelineName": "Pipeline-panel-0001-v1",
"pipelineRef": "https://doi.org/10.48511/workflowhub.workflow.111.1",
"runId": "SRR10903401",
"variantCaller": "GATK4.0"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 89ed443fecde703f259d5ec169ceeede37db72f9 | 2022-03-09T07:58:30 | models/json/beacon-v2-default-model/common/quantity.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"description": "Definition of a quantity class. Provenance: GA4GH Phenopackets v2 `Quantity`",
"properties": {
"referenceRange": {
"$ref": "./referenceRange.json",
"description": "The normal range for the value",
"example": {}
},
"unit": {
"$ref": "./commonDefinitions.json#/definitions/Unit"
},
"value": {
"description": "The value of the quantity in the units",
"type": "number"
}
},
"required": [
"unit",
"value"
],
"title": "Quantity",
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 89ed443fecde703f259d5ec169ceeede37db72f9 | 2022-03-09T07:58:30 | models/json/beacon-v2-default-model/genomicVariations/requestParameters.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"g_variant": {
"properties": {
"alternateBases": {
"$ref": "./requestParametersComponents.json#/definitions/AlternateBases"
},
"aminoacidChange": {
"description": "Aminoacid alteration of interest. Format 1 letter ",
"examples": [
"V600E",
"M734V"
],
"type": "string"
},
"assemblyId": {
"$ref": "./requestParametersComponents.json#/definitions/Assembly"
},
"end": {
"description": "Precise or bracketing the end of the variants of interest:\n* (0-based, exclusive) - see `start`\n* for bracket queries, provide 2 values (e.g. [111,222]).",
"items": {
"format": "int64",
"minimum": 1,
"type": "integer"
},
"maxItems": 2,
"minItems": 0,
"type": "array"
},
"geneId": {
"description": "Gene identifir, it is strongly suggested to use a symbol following the HGNC (https://www.genenames.org) nomenclature.",
"examples": [
"BRAF",
"SCN5A"
],
"type": "string"
},
"mateName": {
"$ref": "./requestParametersComponents.json#/definitions/RefSeqId"
},
"referenceBases": {
"$ref": "./requestParametersComponents.json#/definitions/ReferenceBases"
},
"referenceName": {
"$ref": "./requestParametersComponents.json#/definitions/RefSeqId"
},
"start": {
"description": "Precise or fuzzy start coordinate position(s), allele locus\n(0-based, inclusive).\n* `start` only:\n - for single positions, e.g. the start of a specified sequence\n alteration where the size is given through the specified\n `alternateBases`\n - typical use are queries for SNV and small InDels\n - the use of `start` without an `end` parameter requires the use\n of `alternateBases`\n\n* `start` and `end`:\n - for searching any variant falling fully or partially within the\n range between `start` and `end` (a.k.a. \"range query\")\n - additional use of `variantType` OR `alternateBases` can limit the\n scope of the query\n - by convention, partial overlaps of variants with the indicated\n genomic range are accepted; for specific overlap requirements the\n 4-parammeter \"Bracket Queries\" should be employed\n* use of 2 values in both `start` and `end` for constructing a\n\"Bracket Query\":\n - can be used to match any contiguous genomic interval, e.g. for\n querying imprecise positions\n * identifying all structural variants starting between `start[0]`\n and `start[1]`, and ending between `end[0]` <-> `end[1]`\n * single or double sided precise matches can be achieved by\n setting `start[1]=start[0]+1` and `end[1]=end[0]+1`",
"items": {
"format": "int64",
"minimum": 0,
"type": "integer"
},
"maxItems": 2,
"minItems": 1,
"type": "array"
},
"variantMaxLength": {
"description": "Maximum length in bases of a genomic variant. This is an optional parameter without prescribed use. While a length is commonly available for structural variants such as copy number variations, it is recommended that length based queries should also be supported for variants with indicated referenceBases and alternateBases, to enable length-specific wildcard queries.",
"format": "int64",
"minimum": 1,
"type": "integer"
},
"variantMinLength": {
"description": "Minimum length in bases of a genomic variant. This is an optional parameter without prescribed use. While a length is commonly available for structural variants such as copy number variations, it is recommended that length based queries should also be supported for variants with indicated referenceBases and alternateBases, to enable length-specific wildcard queries.",
"format": "int64",
"minimum": 0,
"type": "integer"
},
"variantType": {
"description": "The `variantType` is used to query variants which are not defined\nthrough a sequence of one or more bases using the `alternateBases`\nparameter. Examples here are e.g. structural variants:\n* DUP\n - increased allelic count of material from the genomic region\n between `start` and `end` positions\n - no assumption about the placement of the additional sequences is\n being made (i.e. no _in situ_ requirement as tandem duplications)\n* DEL: deletion of sequence following `start`\n* BND: breakend, i.e. termination of the allele at position\n `start` or in the `startMin` => `startMax` interval, or fusion\n of the sequence to distant partner\nEither `alternateBases` or `variantType` is required, with the\nexception of range queries (single `start` and `end` parameters).",
"type": "string"
}
},
"type": "object"
}
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | ebb275bb4fe83aadcd8bb63ef9959efc2b7d33b4 | 2022-06-20T14:09:12 | framework/json/common/beaconCommonComponents.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"definitions": {
"$schema": {
"$comment": "TO REVIEW: adding a `format` or `regex` attribute that validates correctly against a file path (relative).",
"description": "Refers to the JSON Schema which describes the set of valid attributes for this particular document type. This attribute is mostly used in schemas that should be tested in Beacon implementations.",
"type": "string"
},
"ApiVersion": {
"description": "an API version.",
"example": "v2.0",
"type": "string"
},
"BeaconError": {
"description": "Beacon-specific error.",
"properties": {
"errorCode": {
"description": "Entry not found",
"examples": [
"404"
],
"format": "int32",
"type": "integer"
},
"errorMessage": {
"examples": [
"the provided parameters are incomplete. 'xyz' is missing."
],
"type": "string"
}
},
"required": [
"errorCode"
],
"type": "object"
},
"BeaconId": {
"description": "the Id of a Beacon. Usually a reversed domain string, but any URI is acceptable. The purpose of this attribute is, in the context of a Beacon network, to disambiguate responses coming from different Beacons.",
"example": "org.example.beacon.v2",
"type": "string"
},
"Exists": {
"description": "Indicator of whether any record was observed in any of the collections queried. This should be non-null.",
"examples": [
true
],
"type": "boolean"
},
"Filters": {
"description": "Ontology based filters. A CURIE syntax is encouraged to be used.",
"example": [
"BTO:0000199",
"PATO:0000383"
],
"items": {
"type": "string"
},
"type": "array"
},
"Granularity": {
"default": "boolean",
"description": "Granularity or level of detail of the response:\n* `boolean`: returns true/false' responses * `count`: adds the total number of positive results found * `aggregated`: returns summary, aggregated or distribution like responses * `record`: returns details for every row. In cases where a Beacon prefers\n to return records with fewer than allattributes, different strategies have\n to be considered w/o adding them to the current design, e.g.:\n - keeping non-mandatory attributes empty\n - Beacon to provide a minimal record definition",
"enum": [
"boolean",
"count",
"aggregated",
"record"
],
"type": "string"
},
"Handover": {
"description": "A handover is a typed link for attaching actionable links to results, non purely informational, requests. The goal of the handovers is to list the different actions available, e.g.:\n* a link to a request access page * linking to a file for download, e.g. a VCF file\nAnother common scenario is to provide a fast summary response (e.g. BeconCountResponse) and to provide access to different endpoints for the entities matched by the query using temporary access tokens in the handover URLs.",
"properties": {
"handoverType": {
"$ref": "#/definitions/HandoverType"
},
"note": {
"description": "An optional text including considerations on the handover link provided.",
"example": "This handover link provides access to a summarized VCF.",
"type": "string"
},
"url": {
"description": "URL endpoint to where the handover process could progress, in RFC3986 format",
"example": "https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0/",
"format": "uri",
"type": "string"
}
},
"required": [
"handoverType",
"url"
],
"type": "object"
},
"HandoverType": {
"$ref": "./ontologyTerm.json",
"description": "Handover type, as an Ontology_term object with CURIE syntax for the `id` value. Use `CUSTOM` for the `id` when no ontology is available.",
"examples": [
{
"id": "EFO:0004157",
"label": "BAM format"
},
{
"id": "CUSTOM",
"label": "download genomic variants in .pgxseg file format"
}
]
},
"IncludeResultsetResponses": {
"default": "HIT",
"description": "Indicator of whether responses from every Resultset should be included in the response to this request or just the ones with positive, negative results or no details at all. If null (not specified), the default value of 'HIT' is assumed. This parameter allows for returning boolean/counting results although the Beacon instance is capable to return record level details.",
"enum": [
"ALL",
"HIT",
"MISS",
"NONE"
],
"examples": [
"ALL",
"HIT",
"MISS",
"NONE"
],
"type": "string"
},
"Info": {
"description": "Placeholder to allow the Beacon to return any additional information that is necessary or could be of interest in relation to the query or the entry returned. It is recommended to encapsulate additional informations in this attribute instead of directly adding attributes at the same level than the others in order to avoid collision in the names of attributes in future versions of the specification.",
"type": "object"
},
"Limit": {
"default": 10,
"description": "Size of the page. Use `0` to return all the results or the maximum allowed by the Beacon, if there is any.",
"example": 10,
"minimum": 0,
"type": "integer"
},
"ListOfHandovers": {
"description": "Set of handovers to be added in one section the response.",
"items": {
"$ref": "#/definitions/Handover",
"description": "Requested schema to be used for individuals in the response."
},
"type": "array"
},
"ListOfSchemas": {
"description": "Set of schemas to be used in the response to a request.",
"items": {
"$ref": "#/definitions/SchemasPerEntity"
},
"type": "array"
},
"NonFilteredQueriesAllowed": {
"default": true,
"description": "Switch that declares if this Beacon instance, for a given entry type, admits queries that does not include any element that restrict returning all the results, like filters, parameters, ids, etc. The default value is 'true' for backward compatibility and for clarity in the request-response dialog.",
"type": "boolean"
},
"NumTotalResults": {
"description": "Total number of results. NOT the number of results returned in this batch, but the total obtained by the query.",
"examples": [
123
],
"minimum": 0,
"type": "integer"
},
"PageToken": {
"description": "A hash or similar that allows the server to use it as a cursor over a query. It could be or not a readable value, like a word or a key. E.g. it could be an encrypted value of primary keys to navigate next and previous page.",
"example": "ab0sc&fe1dd",
"type": "string"
},
"Pagination": {
"description": "Pagination to apply or that has been applied on the results.",
"properties": {
"current_page": {
"$ref": "#/definitions/PageToken",
"description": "Token of the returned page. To be used only in the response to allow the client to check if the returned page is the one requested."
},
"limit": {
"$ref": "#/definitions/Limit"
},
"next_page": {
"$ref": "#/definitions/PageToken",
"description": "Token of the next page. Used to navigate forward. If empty, it is assumed that no more pages are available"
},
"previous_page": {
"$ref": "#/definitions/PageToken",
"description": "Token of the previous page. Used to navigate backwards. If empty, it is assumed that the current page is the first one."
},
"skip": {
"$ref": "#/definitions/Skip"
}
},
"type": "object"
},
"SchemasPerEntity": {
"description": "Schema to be used for the requested entry type in the response.",
"properties": {
"entityType": {
"$comment": "TO REVIEW: Should that refer to a concept d? or would that include an undesired dependency to the configuration?",
"example": "Individual",
"type": "string"
},
"schema": {
"$comment": "TO DO: Add the correct format as 'uri' or 'regex'",
"examples": [
"./ga4gh-beacon-dataset-v2.0.0",
"https://www.example.org/schemas/ga4gh-beacon-dataset-v2.0.0.json"
],
"type": "string"
}
},
"type": "object"
},
"Skip": {
"default": 0,
"description": "* In the request: number of pages to skip * In the response: number of pages that has been skipped",
"example": 0,
"minimum": 0,
"type": "integer"
},
"TestMode": {
"default": false,
"description": "Used for indicating that a request or response is done in a test context e.g. for compliance testing i.e. to evaluate the acceptance/understanding of a request and the structure of the returned response by the Beacon instance. A TRUE `testMode` parameter DOES NOT require that the Beacon instance is a test instance, but that this specific request-response cycle is a testing one. When `true` the Beacon instance MUST respond the request but it SHOULD use virtual or non-sensitive data. Here, what is being evaluated is the acceptance/understanding of a request and the structure of the returned response by the Beacon instance.",
"type": "boolean"
}
},
"description": "Definition of relatively simple components used in different points of the Beacon specification, both in requests and responses, therefore not associated exclusively with one or the other. Separate schema documents are provided for complex components.",
"title": "Beacon Common Components",
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 030747a0ef492bd79dc53d3eaf9f6c16ceae236a | 2022-02-22T13:50:28 | framework/json/responses/beaconInfoResponse.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"description": "Information about the Beacon. Aimed at Beacon clients like web pages or Beacon networks.",
"properties": {
"meta": {
"$ref": "./sections/beaconInformationalResponseMeta.json",
"description": "Information about the response that could be relevant for the Beacon client in order to interpret the results."
},
"response": {
"$ref": "./sections/beaconInfoResults.json",
"description": "Metadata describing a Beacon instance."
}
},
"required": [
"meta",
"response"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 86d8c3bebb92dc892e2560022884e1ddea491821 | 2022-02-22T13:58:39 | framework/json/common/elementWithDescription.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"allOf": [
{
"$ref": "./basicElement.json"
},
{
"properties": {
"description": {
"description": "A textual description for the element.",
"type": "string"
}
},
"type": "object"
}
],
"description": "Definition of the basic element extended with a description.",
"title": "Basic Element including a description",
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 030747a0ef492bd79dc53d3eaf9f6c16ceae236a | 2022-02-22T13:50:28 | framework/json/configuration/entryTypesSchema.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"definitions": {
"EntryTypes": {
"additionalProperties": {
"$ref": "./entryTypeDefinition.json",
"type": "object"
},
"description": "This is a dictionary of the entry types implemented in this Beacon instance.",
"minProperties": 1
}
},
"description": "Schema for the Enrty Types list.",
"properties": {
"entryTypes": {
"$ref": "#/definitions/EntryTypes",
"description": "List of entry types."
}
},
"required": [
"entryTypes"
],
"title": "List of Entry Types schema",
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 86d8c3bebb92dc892e2560022884e1ddea491821 | 2022-02-22T13:58:39 | framework/json/responses/beaconCollectionsResponse.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"description": "Beacon response that includes details about the collections in this Beacon.",
"properties": {
"beaconHandovers": {
"$ref": "../common/beaconCommonComponents.json#/definitions/ListOfHandovers",
"description": "List of handovers that apply to the whole response, not to any resultset or result in particular."
},
"info": {
"$ref": "../common/beaconCommonComponents.json#/definitions/Info",
"description": "Additional details that could be of interest. Provided to clearly enclose any attribute that is not part of the Beacon specification."
},
"meta": {
"$ref": "./sections/beaconResponseMeta.json",
"description": "Information about the response that could be relevant for the Beacon client in order to interpret the results."
},
"response": {
"additionalProperties": true,
"description": "Returning the Beacon Collections list, filtered or unfiltered.",
"properties": {
"collections": {
"items": {
"type": "object"
},
"minItems": 0,
"type": "array"
}
},
"required": [
"collections"
],
"type": "object"
},
"responseSummary": {
"$ref": "./sections/beaconSummaryResponseSection.json",
"description": "Response summary, including Boolean and optionally results count."
}
},
"required": [
"meta",
"responseSummary",
"response"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 89ed443fecde703f259d5ec169ceeede37db72f9 | 2022-03-09T07:58:30 | models/json/beacon-v2-default-model/individuals/examples/individual-MID-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"diseases": [
{
"ageOfOnset": {
"ageGroup": {
"id": "NCIT:C49685",
"label": "Adult 18-65 Years Old"
}
},
"diseaseCode": {
"id": "OMIM:164400",
"label": "Spinocerebellar ataxia 1"
},
"familyHistory": false,
"severityLevel": {
"id": "HP:0012829",
"label": "Profound"
},
"stage": {
"id": "OGMS:0000119",
"label": "acute onset"
}
}
],
"ethnicity": {
"id": "NCIT:C43851",
"label": "European"
},
"geographicOrigin": {
"id": "GAZ:00002955",
"label": "Slovenia"
},
"id": "Ind001",
"measures": [
{
"assayCode": {
"id": "LOINC:26515-7",
"label": "Platelets [#/volume] in Blood"
},
"date": "2017-05-03",
"measurementValue": {
"units": {
"id": "NCIT:C103452",
"label": "Per Milliliter"
},
"value": 55345
},
"observationMoment": {
"age": {
"iso8601duration": "P55Y8M12D"
}
}
}
],
"sex": {
"id": "NCIT:C16576",
"label": "female"
}
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 8e09eabe19cfa57526eefd1765154ec2c985eede | 2022-10-11T11:03:58 | framework/json/responses/sections/beaconCountResponseSection.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "Payload definition for the \"count\" response.",
"properties": {
"exists": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/Exists",
"description": "Indicator of whether any entry was observed. This should be non-null, unless there was an error, in which case a `beaconErrorResponse` is expected instead of this one."
},
"numTotalResults": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/NumTotalResults",
"description": "Total number of results."
}
},
"required": [
"exists",
"numTotalResults"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 89f9aacffcb00b3395ffa9d908cf38c7bb598b5e | 2022-03-23T07:55:42 | models/json/beacon-v2-default-model/common/disease.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "Diseases diagnosed e.g. to an individual, defined by diseaseID, age of onset, stage, level of severity, outcome and the presence of family history. Similarities to GA4GH Phenopackets v2 `Disease`",
"properties": {
"ageOfOnset": {
"$ref": "./timeElement.json",
"examples": [
{
"age": {
"iso8601duration": "P32Y6M1D"
},
"ageGroup": {
"id": "NCIT:C49685",
"label": "Adult 18-65 Years Old"
}
},
{
"ageRange": {
"end": {
"iso8601duration": "P59Y"
},
"start": {
"iso8601duration": "P18Y"
}
}
},
{
"age": {
"iso8601duration": "P2M4D"
}
}
]
},
"diseaseCode": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json",
"description": "Disease identifier. Value from disease ontologies such as HPO, OMIM, Orphanet, MONDO, e.g. lactose intolerance (HP:0004789, ICD10CM:E73). Provenance: GA4GH Phenopackets v2 `Disease.term`",
"examples": [
{
"id": "HP:0004789",
"label": "lactose intolerance"
},
{
"id": "ICD10CM:E73",
"label": "lactose intolerance"
},
{
"id": "OMIM:164400",
"label": "Spinocerebellar ataxia 1"
}
]
},
"familyHistory": {
"description": "Boolean indicating determined or self-reported presence of family history of the disease.",
"example": true,
"type": "boolean"
},
"notes": {
"description": "Unstructured text to describe additional properties of this disease instance.",
"example": "Some free text",
"type": "string"
},
"severityLevel": {
"$ref": "./commonDefinitions.json#/definitions/SeverityLevel"
},
"stage": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json",
"description": "Ontology term from Ontology for General Medical Science (OGMS), e.g. acute onset (OGMS:0000119). Provenance: GA4GH Phenopackets v2 `Disease.disease_stage`",
"examples": [
{
"id": "OGMS:0000119",
"label": "acute onset"
},
{
"id": "OGMS:0000117",
"label": "asymptomatic"
},
{
"id": "OGMS:0000106",
"label": "remission"
}
]
}
},
"required": [
"diseaseCode"
],
"title": "Disease",
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 3e6093cf1b20ac74bc021c315511094f930be1ef | 2022-02-22T11:21:39 | framework/json/common/ontologizedElement.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"allOf": [
{
"$ref": "./elementWithDescription.json"
},
{
"properties": {
"ontologyTermForThisType": {
"$ref": "./ontologyTerm.json"
}
},
"required": [
"ontologyTermForThisType"
],
"type": "object"
}
],
"description": "Definition of the basic element which includes a description and a type defined by an ontology.",
"title": "Element with description and a type defined by an ontology",
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | f3f93ef9f94f0164a185d36dd45045fc1a179c14 | 2022-12-21T19:45:33 | framework/json/responses/beaconErrorResponse.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"description": "An unsuccessful operation.",
"properties": {
"error": {
"$ref": "../common/beaconCommonComponents.json#/definitions/BeaconError"
},
"meta": {
"$ref": "./sections/beaconResponseMeta.json"
}
},
"required": [
"meta",
"error"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 284e82aa022ef5eccc996d957e3af4fbf261c8c8 | 2022-02-24T11:37:28 | framework/json/responses/beaconResultsetsResponse.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"description": "Beacon response that includes record level details, grouped in Resultsets.",
"properties": {
"beaconHandovers": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-unity-testing/main/framework/json/common/beaconCommonComponents.json#/definitions/ListOfHandovers",
"description": "List of handovers that apply to the whole response, not to any resultset or result in particular."
},
"info": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-unity-testing/main/framework/json/common/beaconCommonComponents.json#/definitions/Info",
"description": "Additional details that could be of interest. Provided to clearly enclose any attribute that is not part of the Beacon specification."
},
"meta": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-unity-testing/main/framework/json/responses/sections/beaconResponseMeta.json",
"description": "Information about the response that could be relevant for the Beacon client in order to interpret the results."
},
"response": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-unity-testing/main/framework/json/responses/sections/beaconResultsets.json",
"description": "Response for queries that recovers any result."
},
"responseSummary": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-unity-testing/main/framework/json/responses/sections/beaconSummaryResponseSection.json",
"description": "Response summary, including Boolean and optionally results count."
}
},
"required": [
"meta",
"responseSummary",
"response"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 86d8c3bebb92dc892e2560022884e1ddea491821 | 2022-02-22T13:58:39 | framework/json/responses/ga4gh-service-info-1-0-0-schema.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"definitions": {
"ServiceType": {
"description": "Type of a GA4GH service",
"properties": {
"artifact": {
"description": "Name of the API or GA4GH specification implemented. Official GA4GH types should be assigned as part of standards approval process. Custom artifacts are supported.",
"example": "beacon",
"type": "string"
},
"group": {
"description": "Namespace in reverse domain name format. Use `org.ga4gh` for implementations compliant with official GA4GH specifications. For services with custom APIs not standardized by GA4GH, or implementations diverging from official GA4GH specifications, use a different namespace (e.g. your organization's reverse domain name).",
"example": "org.ga4gh",
"type": "string"
},
"version": {
"description": "Version of the API or specification. GA4GH specifications use semantic versioning.",
"example": "1.0.0",
"type": "string"
}
},
"required": [
"group",
"artifact",
"version"
],
"type": "object"
}
},
"description": "A way for a service to describe basic metadata concerning a service alongside a set of capabilities and/or limitations of the service. More information on [GitHub](https://github.com/ga4gh-discovery/ga4gh-service-info/).",
"properties": {
"contactUrl": {
"description": "URL of the contact for the provider of this service, e.g. a link to a contact form (RFC 3986 format), or an email (RFC 2368 format).",
"example": "mailto:[email protected]",
"format": "uri",
"type": "string"
},
"createdAt": {
"description": "Timestamp describing when the service was first deployed and available (RFC 3339 format)",
"example": "2019-06-04T12:58:19Z",
"format": "date-time",
"type": "string"
},
"description": {
"description": "Description of the service. Should be human readable and provide information about the service.",
"example": "This service provides...",
"type": "string"
},
"documentationUrl": {
"description": "URL of the documentation of this service (RFC 3986 format). This should help someone learn how to use your service, including any specifics required to access data, e.g. authentication.",
"example": "https://docs.myservice.example.com",
"format": "uri",
"type": "string"
},
"environment": {
"description": "Environment the service is running in. Use this to distinguish between production, development and testing/staging deployments. Suggested values are prod, test, dev, staging. However this is advised and not enforced.",
"example": "test",
"type": "string"
},
"id": {
"description": "Unique ID of this service. Reverse domain name notation is recommended, though not required. The identifier should attempt to be globally unique so it can be used in downstream aggregator services e.g. Service Registry.",
"example": "org.ga4gh.myservice",
"type": "string"
},
"name": {
"description": "Name of this service. Should be human readable.",
"example": "My project",
"type": "string"
},
"organization": {
"description": "Organization providing the service",
"properties": {
"name": {
"description": "Name of the organization responsible for the service",
"example": "My organization",
"type": "string"
},
"url": {
"description": "URL of the website of the organization (RFC 3986 format)",
"example": "https://example.com",
"format": "uri",
"type": "string"
}
},
"required": [
"name",
"url"
],
"type": "object"
},
"type": {
"$ref": "#/definitions/ServiceType"
},
"updatedAt": {
"description": "Timestamp describing when the service was last updated (RFC 3339 format)",
"example": "2019-06-04T12:58:19Z",
"format": "date-time",
"type": "string"
},
"version": {
"description": "Version of the service being described. Semantic versioning is recommended, but other identifiers, such as dates or commit hashes, are also allowed. The version should be changed whenever the service is updated.",
"example": "1.0.0",
"type": "string"
}
},
"required": [
"id",
"name",
"type",
"organization",
"version"
],
"title": "GA4GH service-info API specification",
"type": "object",
"version": "1.0.0"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 86d8c3bebb92dc892e2560022884e1ddea491821 | 2022-02-22T13:58:39 | framework/json/common/examples/beaconCommonComponents-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"apiVersion": "v2.0",
"beaconError": {
"errorCode": 404,
"errorMessage": "the provided parameters are incomplete. 'xyz' is missing."
},
"beaconId": "org.example.beacon.v2",
"exists": true,
"filters": [
"BTO:0000199",
"PATO:0000383"
],
"handover": {
"handoverType": {
"id": "EFO:0004157",
"label": "BAM format"
},
"note": "This handover link provides access to a summarized VCF.",
"url": "https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0"
},
"handoverType": {
"id": "EFO:0004157",
"label": "BAM format"
},
"includeResultsetResponses": "HIT",
"info": {},
"listOfHandovers": [
{
"handoverType": {
"id": "EFO:0004157",
"label": "BAM format"
},
"note": "This handover link provides access to a summarized VCF.",
"url": "https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0"
},
{
"handoverType": {
"id": "EFO:0004157",
"label": "BAM format"
},
"note": "This handover link provides access to a summarized VCF.",
"url": "https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0"
}
],
"listOfSchemas": [
{
"entityType": "EntryTypeA",
"schema": "entry-typeA-schema-v0.1"
},
{
"entityType": "EntryTypeB",
"schema": "entry-typeB-schema-v1.0"
}
],
"numTotalResults": 123,
"pagination": {
"limit": 10,
"skip": 0
},
"schemasPerEntity": {
"entityType": "Individual",
"schema": "ga4gh-phenopacket-individual-v0.1"
}
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 2c53ba10fba1bf39152e286d3a6edc756de7f6fc | 2022-04-05T15:50:47 | models/json/beacon-v2-default-model/genomicVariations/examples/genomicVariant-MID-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"frequencyInPopulations": [
{
"frequencies": [
{
"alleleFrequency": 2.939e-05,
"population": "European (non-Finish)"
},
{
"alleleFrequency": 0,
"population": "Other"
}
],
"source": "gnomaD Genomes",
"sourceReference": "https://gnomad.broadinstitute.org/",
"version": "v3.1.1"
},
{
"frequencies": [
{
"alleleFrequency": 9e-05,
"population": "Total"
},
{
"alleleFrequency": 6e-05,
"population": "European"
},
{
"alleleFrequency": 0,
"population": "African"
}
],
"source": "ALFA",
"sourceReference": "https://www.ncbi.nlm.nih.gov/snp/docs/gsr/alfa/",
"version": "20201027095038"
}
],
"identifiers": {
"clinVarIds": [
"434136",
"VCV000440707.6"
],
"genomicHGVSId": "NC_000001.11:g.55039979G>A",
"proteinHGVSIds": [
"NP_777596.2:p.Glu48Lys"
],
"transcriptHGVSIds": [
"NM_174936.4:c.142G>A"
],
"variantAlternativeIds": [
"dbSNP:rs3975092470",
"ClinGen: CA340482854"
]
},
"molecularAttributes": {
"aminoacidChanges": [
"E48K"
],
"geneIds": [
"PCSK9",
"LRG_275"
],
"molecularEffects": [
{
"id": "ENSGLOSSARY:0000150",
"label": "Missense variant"
}
]
},
"variantInternalId": "var123",
"variantLevelData": {
"clinicalInterpretations": [
{
"category": {
"id": "MONDO:0000001",
"label": "disease or disorder"
},
"clinicalRelevance": "pathogenic",
"conditionId": "famchol1",
"effect": {
"id": "MONDO:0007750",
"label": "Familial hypercholesterolemia 1"
}
},
{
"category": {
"id": "MONDO:0000001",
"label": "disease or disorder"
},
"clinicalRelevance": "uncertain significance",
"conditionId": "famchol3",
"effect": {
"id": "MONDO:0011369",
"label": "hypercholesterolemia, autosomal dominant, 3"
}
}
]
},
"variation": {
"alternateBases": "A",
"location": {
"interval": {
"end": {
"type": "Number",
"value": 55039980
},
"start": {
"type": "Number",
"value": 55039979
},
"type": "SequenceInterval"
},
"sequence_id": "refseq:NC_000001.11",
"type": "SequenceLocation"
},
"referenceBases": "G",
"variantType": "SNP"
}
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 89ed443fecde703f259d5ec169ceeede37db72f9 | 2022-03-09T07:58:30 | models/json/beacon-v2-default-model/common/measurement.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"description": "Definition of a measurement class. Provenance: GA4GH Phenopackets v2 `Measurement`",
"properties": {
"assayCode": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-unity-testing/main/framework/json/common/ontologyTerm.json",
"description": "Class that describes the assay used to produce the measurement. Renamed compared to GA4GH Phenopackets v2 `Measurement.assay`",
"example": {
"id": "LOINC:26515-7",
"label": "Platelets [#/volume] in Blood"
}
},
"date": {
"description": "Date of measurement. Addition compared to Phenopackets model.",
"format": "date",
"type": "string"
},
"measurementValue": {
"description": "The result of the measurement",
"oneOf": [
{
"$ref": "./value.json"
},
{
"$ref": "./complexValue.json"
}
]
},
"notes": {
"description": "Unstructured text to describe this measurement. Addition compared to Phenopackets model.",
"example": "Some free text",
"type": "string"
},
"observationMoment": {
"$ref": "./timeElement.json",
"description": "Moment in time at which measurement was performed. RECOMMENDED. Renamed compared to GA4GH Phenopackets v2 `Measurement.time_observed`",
"example": {
"age": {
"iso8601duration": "P53Y8M"
}
}
},
"procedure": {
"$ref": "./procedure.json",
"description": "Clinical procedure performed to acquire the sample used for the measurement",
"example": {
"code": {
"id": "NCIT:C5189",
"label": "Radical Cystoprostatectomy"
}
}
}
},
"required": [
"assayCode",
"measurementValue"
],
"title": "Measurement",
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 34836304030edee0bd7324766e9ae305671d45b7 | 2022-11-16T12:34:10 | models/json/beacon-v2-default-model/genomicVariations/requestParametersComponents.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"definitions": {
"AlternateBases": {
"description": "Alternate bases for this variant (starting from `start`). * Accepted values: `[ACGTN]*` * N is a wildcard, that denotes the position of any base,\n and can be used as a standalone base of any type or within a partially known\n sequence. As example, a query of `ANNT` the Ns can take take any form of [ACGT]\n and will match `ANNT`, `ACNT`, `ACCT`, `ACGT` ... and so forth.\n* an *empty value* is used in the case of deletions with the maximally trimmed,\n deleted sequence being indicated in `ReferenceBases`\n* Categorical variant queries, e.g. such *not* being represented through\n sequence & position, make use of the `variantType` parameter.\n* either `alternateBases` or `variantType` is required.",
"pattern": "^([ACGTUNRYSWKMBDHV\\-\\.]*)$",
"type": "string"
},
"Assembly": {
"description": "Genomic assembly accession and version as RefSqeq assembly accession (e.g. \"GCF_000001405.39\") or a versioned assembly name or synonym such as UCSC Genome Browser assembly (e.g. \"hg38\") or Genome Reference Consortium Human (e.g. \"GRCh38.p13\") names.",
"example": [
"GCF_000001405.39",
"hg38",
"GRCh38.p13"
],
"type": "string"
},
"RefSeqId": {
"description": "Reference sequence id for genomic reference sequence in which variant coordinates are given, e.g. \"refseq:NC_000009.12\" for human chromosome 9 in the GRCh38 assembly. The use of the assembly specific RefSeqId is recommended although alternatively names, synonymous or aliases e.g. \"chr9\" could be used in conjunction with an `Assembly` parameter.",
"example": [
"refseq:NC_000009.12",
"chr9",
"NC_012920.1"
],
"type": "string"
},
"ReferenceBases": {
"description": "Reference bases for this variant (starting from `start`). * Accepted values: `[ACGTN]*` * N is a wildcard, that denotes the position of any base,\n and can be used as a standalone base of any type or within a partially known\n sequence. As example, a query of `ANNT` the Ns can take take any form of [ACGT]\n and will match `ANNT`, `ACNT`, `ACCT`, `ACGT` ... and so forth.\n* an *empty value* is used in the case of insertions with the maximally trimmed, inserted\n sequence being indicated in `AlternateBases`",
"pattern": "^([ACGTUNRYSWKMBDHV\\-\\.]*)$",
"type": "string"
}
},
"description": "Component definitions used in `requestParameters`."
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 89f9aacffcb00b3395ffa9d908cf38c7bb598b5e | 2022-03-23T07:55:42 | models/json/beacon-v2-default-model/common/value.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "Definition of a value class. Provenance: GA4GH Phenopackets v2 `Value`",
"oneOf": [
{
"$ref": "./quantity.json"
},
{
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json"
}
],
"title": "Value",
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 030747a0ef492bd79dc53d3eaf9f6c16ceae236a | 2022-02-22T13:50:28 | framework/json/responses/sections/beaconResponseMeta.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "Information about the response that could be relevant for the Beacon client in order to interpret the results.",
"properties": {
"apiVersion": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/ApiVersion",
"description": "Version of the API."
},
"beaconId": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/BeaconId",
"description": "Identifier of the beacon, as defined in `Beacon`."
},
"receivedRequestSummary": {
"$ref": "./beaconReceivedRequestSummary.json",
"description": "Section of the response that summarize the request received as it has been interpreted by teh Beacon server."
},
"returnedGranularity": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/Granularity",
"description": "Requested granularity. Targeted Beacon could respond or not with the requested granularity. E.g. record level granularity could be requested, but the Beacon could respond only with boolean or count results."
},
"returnedSchemas": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/ListOfSchemas"
},
"testMode": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/TestMode",
"description": "Used for indicating that a response is returned in a test context. Purposed for compliance testing. Information returned could be fake."
}
},
"required": [
"beaconId",
"apiVersion",
"returnedSchemas",
"returnedGranularity",
"receivedRequestSummary"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 030747a0ef492bd79dc53d3eaf9f6c16ceae236a | 2022-02-22T13:50:28 | framework/json/common/referenceToAnSchema.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"allOf": [
{
"$ref": "./elementWithDescription.json"
},
{
"properties": {
"referenceToSchemaDefinition": {
"$comment": "this should map to a resolvable reference",
"type": "string"
},
"schemaVersion": {
"description": "this version reference is only used for readability in the client. The 'referenceToSchemaDefinition' property is the only source for determining the actual schema used.",
"type": "string"
}
},
"required": [
"referenceToSchemaDefinition"
],
"type": "object"
}
],
"description": "Definition of an annotated URL address or a file reference.",
"title": "An annotated URL address or a file reference",
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 3f8ea95c7c6cabb47a4d3abbbdbf92591ae6bfff | 2022-11-10T07:55:53 | framework/json/requests/beaconRequestBody.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"definitions": {
"BeaconQuery": {
"description": "Parameters to limit the list of returned results.",
"properties": {
"filters": {
"$ref": "./filteringTerms.json",
"description": "Ontology based filters. Using CURIE syntax is encouraged."
},
"includeResultsetResponses": {
"$ref": "../common/beaconCommonComponents.json#/definitions/IncludeResultsetResponses"
},
"pagination": {
"$ref": "../common/beaconCommonComponents.json#/definitions/Pagination",
"description": "Pagination parameters applied to response documents, in case of record level granularity."
},
"requestParameters": {
"$ref": "./requestParameters.json",
"description": "Parameters used for the entry type specific query elements."
},
"requestedGranularity": {
"$ref": "../common/beaconCommonComponents.json#/definitions/Granularity",
"description": "Requested granularity for the response. Beacons do not have to respond with the requested granularity, e.g. may respond with count results although record level granularity had been requested but indicate the granularity of the response in the response's metadata."
},
"testMode": {
"$ref": "../common/beaconCommonComponents.json#/definitions/TestMode",
"description": "Used for indicating that a request or response is done in a test context."
}
},
"type": "object"
}
},
"description": "Schema for the Beacon request. It is named `RequestBody` to keep the same nomenclature used by OpenAPI v3, but it actually contains the definition of the whole HTTP POST request payload.",
"properties": {
"$schema": {
"$ref": "../common/beaconCommonComponents.json#/definitions/$schema"
},
"meta": {
"$ref": "./beaconRequestMeta.json",
"description": "Information relevant for building the response."
},
"query": {
"$ref": "#/definitions/BeaconQuery"
}
},
"required": [
"meta"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 030747a0ef492bd79dc53d3eaf9f6c16ceae236a | 2022-02-22T13:50:28 | framework/json/configuration/examples/entriesCollectionDefinition_example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"aCollectionOf": [
{
"id": "exampleEntry",
"name": "Example entries"
}
],
"additionallySupportedSchemas": [
{
"description": "ATLAS is an open source software tool for researchers to conduct scientific analyses on standardized observational data converted to the OMOP Common Data Model V5.",
"id": "ohdsi-atlas-cohort",
"name": "OHDSI ATLAS Cohort",
"referenceToSchemaDefinition": "https://raw.githubusercontent.com/OHDSIBr/ATLAS-JSON-Schema/2.7.4/single/atlas_cohort_definition.json",
"schemaVersion": "2.7.4"
}
],
"defaultSchema": {
"id": "datasetDefaultSchema",
"name": "Default schema for datasets",
"referenceToSchemaDefinition": "./datasets/defaultSchema.json",
"schemaVersion": "v.2"
},
"description": "A Dataset is a collection of records, like rows in a database or cards in a cardholder.",
"endpoint": "/datasets",
"filteringTermsReference": "./datasets/filteringTerms.json",
"id": "dataset",
"name": "Dataset",
"ontologyTermForThisType": {
"id": "NCIT:C47824",
"label": "Data set"
},
"partOfSpecification": "Beacon v2.0"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 89ed443fecde703f259d5ec169ceeede37db72f9 | 2022-03-09T07:58:30 | models/json/beacon-v2-default-model/datasets/filteringTerms.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"filteringTerms": [
{
"ftType": "ontologyTerm",
"id": "DUO:0000006",
"label": "health or medical or biomedical research",
"version": "2021-02-23"
}
]
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 030747a0ef492bd79dc53d3eaf9f6c16ceae236a | 2022-02-22T13:50:28 | framework/json/responses/beaconCountResponse.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "Complete definition for a Response that does not include record level details and just `boolean` or `count` responses.",
"properties": {
"beaconHandovers": {
"$ref": "../common/beaconCommonComponents.json#/definitions/ListOfHandovers",
"description": "List of handovers that apply to the whole response, not to any resultset or result in particular."
},
"info": {
"$ref": "../common/beaconCommonComponents.json#/definitions/Info",
"description": "Additional details that could be of interest. Provided to clearly enclose any attribute that is not part of the Beacon specification."
},
"meta": {
"$ref": "./sections/beaconResponseMeta.json",
"description": "Information about the response that could be relevant for the Beacon client in order to interpret the results."
},
"responseSummary": {
"$ref": "./sections/beaconSummaryResponseSection.json",
"description": "Response summary, including Boolean and optionally results count."
}
},
"required": [
"meta",
"responseSummary"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 89ed443fecde703f259d5ec169ceeede37db72f9 | 2022-03-09T07:58:30 | models/json/beacon-v2-default-model/beaconConfiguration.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"entryTypes": {
"analysis": {
"additionallySupportedSchemas": [],
"defaultSchema": {
"id": "ga4gh-beacon-analysis-v2.0.0",
"name": "Default schema for a bioinformatics analysis",
"referenceToSchemaDefinition": "https://exampleBeacons.org/analyses/defaultSchema.json",
"schemaVersion": "v2.0.0"
},
"description": "Apply analytical methods to existing data of a specific type.",
"id": "analysis",
"name": "Bioinformatics analysis",
"ontologyTermForThisType": {
"id": "edam:operation_2945",
"label": "Analysis"
},
"partOfSpecification": "Beacon v2.0.0"
},
"biosample": {
"additionallySupportedSchemas": [],
"defaultSchema": {
"id": "ga4gh-beacon-biosample-v2.0.0",
"name": "Default schema for a biological sample",
"referenceToSchemaDefinition": "https://exampleBeacons.org/biosamples/defaultSchema.json",
"schemaVersion": "v2.0.0"
},
"description": "Any material sample taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes, including a sample obtained from a living organism or taken from the biological object after halting of all its life functions. Biospecimen can contain one or more components including but not limited to cellular molecules, cells, tissues, organs, body fluids, embryos, and body excretory products. [ NCI ]",
"id": "biosample",
"name": "Biological Sample",
"ontologyTermForThisType": {
"id": "NCIT:C70699",
"label": "Biospecimen"
},
"partOfSpecification": "Beacon v2.0.0"
},
"cohort": {
"aCollectionOf": [
{
"id": "individual",
"name": "Individuals"
}
],
"additionalSupportedSchemas": [],
"defaultSchema": {
"id": "ga4gh-beacon-cohort-v2.0.0",
"name": "Default schema for cohorts",
"referenceToSchemaDefinition": "https://exampleBeacons.org/cohorts/defaultSchema.json",
"schemaVersion": "v2.0.0"
},
"description": "A group of individuals, identified by a common characteristic. [ NCI ]",
"id": "cohort",
"name": "Cohort",
"ontologyTermForThisType": {
"id": "NCIT:C61512",
"label": "Cohort"
},
"partOfSpecification": "Beacon v2.0.0"
},
"dataset": {
"aCollectionOf": [
{
"id": "genomicVariant",
"name": "Genomic Variants"
}
],
"additionalSupportedSchemas": [],
"defaultSchema": {
"id": "ga4gh-beacon-dataset-v2.0.0",
"name": "Default schema for datasets",
"referenceToSchemaDefinition": "https://exampleBeacons.org/datasets/defaultSchema.json",
"schemaVersion": "v2.0.0"
},
"description": "A Dataset is a collection of related sets of information, e.g. genomic variations together with associated procedural and biological metadata. In a Beacon context, a datasets may consist of information generated in a specific study or project, or represent the main content of the Beacon resource.",
"id": "dataset",
"name": "Dataset",
"ontologyTermForThisType": {
"id": "NCIT:C47824",
"label": "Data set"
},
"partOfSpecification": "Beacon v2.0.0"
},
"genomicVariant": {
"additionallySupportedSchemas": [],
"defaultSchema": {
"id": "ga4gh-beacon-variant-v2.0.0",
"name": "Default schema for a genomic variation",
"referenceToSchemaDefinition": "https://exampleBeacons.org/genomicVariations/defaultSchema.json",
"schemaVersion": "v2.0.0"
},
"description": "The location of a sequence.",
"id": "genomicVariant",
"name": "Genomic Variants",
"ontologyTermForThisType": {
"id": "ENSGLOSSARY:0000092",
"label": "Variant"
},
"partOfSpecification": "Beacon v2.0.0"
},
"individual": {
"additionallySupportedSchemas": [],
"defaultSchema": {
"id": "ga4gh-beacon-individual-v2.0.0",
"name": "Default schema for an individual",
"referenceToSchemaDefinition": "https://exampleBeacons.org/individuals/defaultSchema.json",
"schemaVersion": "v2.0.0"
},
"description": "A human being. It could be a Patient, a Tissue Donor, a Participant, a Human Study Subject, etc.",
"id": "individual",
"name": "Individual",
"ontologyTermForThisType": {
"id": "NCIT:C25190",
"label": "Person"
},
"partOfSpecification": "Beacon v2.0.0"
},
"run": {
"additionallySupportedSchemas": [],
"defaultSchema": {
"id": "ga4gh-beacon-run-v2.0.0",
"name": "Default schema for a sequencing run",
"referenceToSchemaDefinition": "https://exampleBeacons.org/runs/defaultSchema.json",
"schemaVersion": "v2.0.0"
},
"description": "The valid and completed operation of a high-throughput sequencing instrument for a single sequencing process. [ NCI ]",
"id": "run",
"name": "Sequencing run",
"ontologyTermForThisType": {
"id": "NCIT:C148088",
"label": "Sequencing run"
},
"partOfSpecification": "Beacon v2.0.0"
}
},
"maturityAttributes": {
"productionStatus": "DEV"
},
"securityAttributes": {
"defaultGranularity": "record",
"securityLevels": [
"PUBLIC"
]
}
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 76473abf60e91dc993a3e1cd2e63bca8b64c30e9 | 2022-07-01T12:47:44 | framework/json/common/ontologyTerm.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"description": "Definition of an ontology term.",
"properties": {
"id": {
"$ref": "./beaconCommonComponents.json#/definitions/CURIE"
},
"label": {
"description": "The text that describes the term. By default it could be the preferred text of the term, but is it acceptable to customize it for a clearer description and understanding of the term in an specific context.",
"type": "string"
}
},
"required": [
"id"
],
"title": "Ontology Term",
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 89ed443fecde703f259d5ec169ceeede37db72f9 | 2022-03-09T07:58:30 | models/json/beacon-v2-default-model/individuals/examples/individual-with-pedigree-MID-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"diseases": [
{
"ageOfOnset": {
"ageGroup": {
"id": "NCIT:C16731",
"label": "Newborn"
}
},
"diseaseCode": {
"id": "HP:0001645",
"label": "Sudden cardiac death"
},
"familyHistory": true,
"severityLevel": {
"id": "HP:0012828",
"label": "Severe"
}
}
],
"ethnicity": {
"id": "NCIT:C43851",
"label": "European"
},
"geographicOrigin": {
"id": "GAZ:00002586",
"label": "State of Wisconsin"
},
"id": "Ind001",
"pedigrees": [
{
"disease": {
"diseaseCode": {
"id": "HP:0001645",
"label": "Sudden cardiac death"
}
},
"id": "SCD-Pedigree001",
"members": [
{
"affected": true,
"memberId": "Ind001",
"role": {
"id": "NCIT:C64435",
"label": "Proband"
}
},
{
"affected": false,
"memberId": "Ind011",
"role": {
"id": "NCIT:C96572",
"label": "Biological Father"
}
},
{
"affected": false,
"memberId": "Ind012",
"role": {
"id": "NCIT:C96572",
"label": "Biological Father"
}
},
{
"affected": false,
"memberId": "Ind022",
"role": {
"id": "NCIT:C111201",
"label": "Full Brother"
}
}
],
"numSubjects": 4
}
],
"sex": {
"id": "NCIT:C16576",
"label": "female"
}
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 89ed443fecde703f259d5ec169ceeede37db72f9 | 2022-03-09T07:58:30 | models/json/beacon-v2-default-model/individuals/examples/individual-MIN-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"id": "Ind001",
"sex": {
"id": "NCIT:C16576",
"label": "female"
}
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 89ed443fecde703f259d5ec169ceeede37db72f9 | 2022-03-09T07:58:30 | models/json/beacon-v2-default-model/individuals/filteringTerms.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"filteringTerms": []
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 5a418fe5a8fa96eeac46d945550cc599cfb3fc3e | 2022-06-21T09:10:10 | framework/json/requests/filteringTerms.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"definitions": {
"AlphanumericFilter": {
"description": "Filter results based on operators and values applied to alphanumeric fields.",
"properties": {
"id": {
"description": "Field identfier to be queried.",
"example": "age",
"type": "string"
},
"operator": {
"default": "=",
"description": "Defines how the value relates to the field `id`.",
"enum": [
"=",
"<",
">",
"!",
">=",
"<="
],
"example": ">",
"type": "string"
},
"scope": {
"description": "The entry type to which the filter applies",
"example": "biosamples",
"type": "string"
},
"value": {
"description": "Alphanumeric search term to be used within the query which can contain wildcard characters (%) to denote any number of unknown characters. Values can be assocatied with units if applicable.",
"example": "P70Y",
"type": "string"
}
},
"required": [
"id",
"operator",
"value"
],
"type": "object"
},
"CustomFilter": {
"description": "Filter results to include records that contain a custom term defined by this Beacon.",
"properties": {
"id": {
"description": "Custom filter terms should contain a unique identifier.",
"example": "demographic.ethnicity:asian",
"type": "string"
},
"scope": {
"description": "The entry type to which the filter applies",
"example": "biosamples",
"type": "string"
}
},
"required": [
"id"
],
"type": "object"
},
"OntologyFilter": {
"description": "Filter results to include records that contain a specific ontology term.",
"properties": {
"id": {
"description": "Term ID to be queried, using CURIE syntax where possible.",
"example": "HP:0002664",
"type": "string"
},
"includeDescendantTerms": {
"default": true,
"description": "Define if the Beacon should implement the ontology hierarchy, thus query the descendant terms of `id`.",
"type": "boolean"
},
"scope": {
"description": "The entry type to which the filter applies",
"example": "biosamples",
"type": "string"
},
"similarity": {
"default": "exact",
"description": "Allow the Beacon to return results which do not match the filter exactly, but do match to a certain degree of similarity. The Beacon defines the semantic similarity model implemented and how to apply the thresholds of 'high', 'medium' and 'low' similarity.",
"enum": [
"exact",
"high",
"medium",
"low"
],
"type": "string"
}
},
"required": [
"id"
],
"type": "object"
}
},
"description": "Filtering terms are the main means to select subsets of records from a Beacon response. While the name implies the application to a generated response, in practice implementations may apply them at the query stage. Note: In the processing of Beacon v2.0 requests multiple filters are assumed to be chained by the logical AND operator.",
"items": {
"anyOf": [
{
"$ref": "#/definitions/OntologyFilter"
},
{
"$ref": "#/definitions/AlphanumericFilter"
},
{
"$ref": "#/definitions/CustomFilter"
}
]
},
"title": "Filtering Term Element",
"type": "array"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | a0b7743ed0f1d86efbe14edf193be47dbc499507 | 2022-03-11T16:25:38 | models/json/beacon-v2-default-model/common/commonDefinitions.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"definitions": {
"Ethnicity": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-unity-testing/main/framework/json/common/ontologyTerm.json",
"description": "Ethnic background of the individual. Value from NCIT Race (NCIT:C17049) ontology term descendants, e.g. NCIT:C126531 (Latin American). A geographic ancestral origin category that is assigned to a population group based mainly on physical characteristics that are thought to be distinct and inherent. [ NCI ] ",
"examples": [
{
"id": "NCIT:C42331",
"label": "African"
},
{
"id": "NCIT:C41260",
"label": "Asian"
},
{
"id": "NCIT:C126535",
"label": "Australian"
},
{
"id": "NCIT:C43851",
"label": "European"
},
{
"id": "NCIT:C77812",
"label": "North American"
},
{
"id": "NCIT:C126531",
"label": "Latin American"
},
{
"id": "NCIT:C104495",
"label": "Other race"
}
]
},
"GeographicLocation": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-unity-testing/main/framework/json/common/ontologyTerm.json",
"description": "Country or region of origin of the individual (birthplace or residence place regardless of ethnic origin). Value from GAZ Geographic Location ontology (GAZ:00000448), e.g. GAZ:00002459 (United States of America).",
"examples": [
{
"id": "GAZ:00002955",
"label": "Slovenia"
},
{
"id": "GAZ:00002459",
"label": "United States of America"
},
{
"id": "GAZ:00316959",
"label": "Municipality of El Masnou"
},
{
"id": "GAZ:00000460",
"label": "Eurasia"
}
]
},
"SeverityLevel": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-unity-testing/main/framework/json/common/ontologyTerm.json",
"description": "Level/severity ontology when and as applicable to phenotype observed. Value from Human Phenotype Ontology (HP:0012824), e.g `mild`. The intensity or degree of a manifestation. [ HPO:probinson ] ",
"examples": [
{
"id": "HP:0012825",
"label": "Severe"
},
{
"id": "HP:0012829",
"label": "Profound"
},
{
"id": "HP:0012826",
"label": "Moderate"
},
{
"id": "HP:0012825",
"label": "Mild"
},
{
"id": "HP:0012827",
"label": "Bordeline"
}
]
},
"Sex": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-unity-testing/main/framework/json/common/ontologyTerm.json",
"description": "Sex of the individual. Value from NCIT General Qualifier (NCIT:C27993): 'unknown' (not assessed or not available) (NCIT:C17998), 'female' (NCIT:C16576), or 'male', (NCIT:C20197).",
"examples": [
{
"id": "NCIT:C16576",
"label": "female"
},
{
"id": "NCIT:C20197",
"label": "male"
},
{
"id": "NCIT:C1799",
"label": "unknown"
}
]
},
"Unit": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-unity-testing/main/framework/json/common/ontologyTerm.json",
"description": "The kind of unit. Recommended from NCIT Unit of Category ontology term (NCIT:C42568) descendants",
"examples": [
{
"id": "NCIT:C70575",
"label": "Roentgen"
},
{
"id": "NCIT:C28252",
"label": "Kilogram"
},
{
"id": "NCIT:C28253",
"label": "Milligram"
}
]
}
},
"description": "Definitions for concepts used in several entry types, but that having only one property are not complex enough to require a full independent schema document.",
"title": "Common Definitions"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 89f9aacffcb00b3395ffa9d908cf38c7bb598b5e | 2022-03-23T07:55:42 | models/json/beacon-v2-default-model/common/commonDefinitions.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"definitions": {
"Ethnicity": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json",
"description": "Ethnic background of the individual. Recommended is the use of a value from NCIT Race (NCIT:C17049) ontology term descendants, e.g. NCIT:C126531 (Latin American). A geographic ancestral origin category that is assigned to a population group based mainly on physical characteristics that are thought to be distinct and inherent. [ NCI ]",
"examples": [
{
"id": "NCIT:C42331",
"label": "African"
},
{
"id": "NCIT:C41260",
"label": "Asian"
},
{
"id": "NCIT:C126535",
"label": "Australian"
},
{
"id": "NCIT:C43851",
"label": "European"
},
{
"id": "NCIT:C77812",
"label": "North American"
},
{
"id": "NCIT:C126531",
"label": "Latin American"
},
{
"id": "NCIT:C104495",
"label": "Other race"
}
]
},
"GeographicLocation": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json",
"description": "Country or region of origin of the individual (birthplace or residence place regardless of ethnic origin). Value from GAZ Geographic Location ontology (GAZ:00000448), e.g. GAZ:00002459 (United States of America).",
"examples": [
{
"id": "GAZ:00002955",
"label": "Slovenia"
},
{
"id": "GAZ:00002459",
"label": "United States of America"
},
{
"id": "GAZ:00316959",
"label": "Municipality of El Masnou"
},
{
"id": "GAZ:00000460",
"label": "Eurasia"
}
]
},
"KaryotypicSex": {
"$comments": "Compares to https://github.com/phenopackets/phenopacket-schema/blob/master/docs/karyotypicsex.rst",
"default": "UNKNOWN_KARYOTYPE",
"description": "The chromosomal sex of an individual represented from a selection of options. The values correspond to the ordinal values in the Phenopackets schema where: 0 - UNKNOWN_KARYOTYPE (Untyped or inconclusive karyotyping); 1 - XX (Female); 2 - XY (Male); 3 - XO (Single X chromosome only); 4 - XXY (Two X and one Y chromosome); 5 - XXX (Three X chromosomes); 6 - XXYY (Two X chromosomes and two Y chromosomes); 7 - XXXY (Three X chromosomes and one Y chromosome); 8 - XXXX (Four X chromosomes); 9 - XYY (One X and two Y chromosomes); 10 - OTHER_KARYOTYPE (None of the above types)",
"enum": [
"UNKNOWN_KARYOTYPE",
"XX",
"XY",
"XO",
"XXY",
"XXX",
"XXYY",
"XXXY",
"XXXX",
"XYY",
"OTHER_KARYOTYPE"
],
"type": "string"
},
"SeverityLevel": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json",
"description": "Level/severity ontology when and as applicable to phenotype observed. Value from Human Phenotype Ontology (HP:0012824), e.g `mild`. The intensity or degree of a manifestation. [ HPO:probinson ] ",
"examples": [
{
"id": "HP:0012825",
"label": "Severe"
},
{
"id": "HP:0012829",
"label": "Profound"
},
{
"id": "HP:0012826",
"label": "Moderate"
},
{
"id": "HP:0012825",
"label": "Mild"
},
{
"id": "HP:0012827",
"label": "Bordeline"
}
]
},
"Sex": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json",
"description": "Sex of the individual. Recommended values from NCIT General Qualifier (NCIT:C27993): \"unknown\" (not assessed or not available) - NCIT:C17998; \"female\" - NCIT:C16576; \"male\" - NCIT:C20197",
"examples": [
{
"id": "NCIT:C16576",
"label": "female"
},
{
"id": "NCIT:C20197",
"label": "male"
},
{
"id": "NCIT:C1799",
"label": "unknown"
}
]
},
"Unit": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json",
"description": "The kind of unit. Recommended from NCIT Unit of Category ontology term (NCIT:C42568) descendants",
"examples": [
{
"id": "NCIT:C70575",
"label": "Roentgen"
},
{
"id": "NCIT:C28252",
"label": "Kilogram"
},
{
"id": "NCIT:C28253",
"label": "Milligram"
}
]
}
},
"description": "Definitions for concepts used in several entry types, but that having only one property are not complex enough to require a full independent schema document.",
"title": "Common Definitions"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 89f9aacffcb00b3395ffa9d908cf38c7bb598b5e | 2022-03-23T07:55:42 | framework/json/responses/beaconResultsetsResponse.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"description": "Beacon response that includes record level details, grouped in Resultsets.",
"properties": {
"beaconHandovers": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/ListOfHandovers",
"description": "List of handovers that apply to the whole response, not to any resultset or result in particular."
},
"info": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Info",
"description": "Additional details that could be of interest. Provided to clearly enclose any attribute that is not part of the Beacon specification."
},
"meta": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/sections/beaconResponseMeta.json",
"description": "Information about the response that could be relevant for the Beacon client in order to interpret the results."
},
"response": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/sections/beaconResultsets.json",
"description": "Response for queries that recovers any result."
},
"responseSummary": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/sections/beaconSummaryResponseSection.json",
"description": "Response summary, including Boolean and optionally results count."
}
},
"required": [
"meta",
"responseSummary",
"response"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 89f9aacffcb00b3395ffa9d908cf38c7bb598b5e | 2022-03-23T07:55:42 | framework/json/responses/examples-fullDocuments/beaconConfigurationResponse-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"info": {},
"meta": {
"apiVersion": "string",
"beaconId": "string",
"returnedSchemas": [
{
"entityType": "info",
"schema": "beacon-map-v2.0.0"
}
]
},
"response": {
"$schema": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/configuration/beaconConfigurationSchema.json",
"entryTypes": {
"dataset": {
"aCollectionOf": [
{
"id": "exampleEntry",
"name": "Example entries"
}
],
"additionallySupportedSchemas": [],
"defaultSchema": {
"id": "datasetDefaultSchema",
"name": "Default schema for datasets",
"referenceToSchemaDefinition": "./datasets/defaultSchema.json",
"schemaVersion": "v.2"
},
"description": "A Dataset is a collection of records, like rows in a database or cards in a cardholder.",
"endpoint": "/datasets",
"filteringTermsReference": "./datasets/filteringTerms.json",
"id": "dataset",
"name": "Dataset",
"ontologyTermForThisType": {
"id": "NCIT:C47824",
"label": "Data set"
},
"partOfSpecification": "Beacon v2.0"
},
"exampleEntry": {
"additionallySupportedSchemas": [],
"defaultSchema": {
"id": "ExampleEntryTypeDefaultschema",
"name": "Default schema for an example entries",
"referenceToSchemaDefinition": "./exampleEntry/defaultSchema.json",
"schemaVersion": "v.2"
},
"description": "A generic entry type to allow testing and playing with the specification.",
"endpoint": "./exampleEntries",
"filteringTermsReference": "./exampleEntry/filteringTerms.json",
"id": "exampleEntry",
"name": "Example Entry",
"ontologyTermForThisType": {
"id": "NCIT:C20181",
"label": "Conceptual Entity"
},
"partOfSpecification": "Beacon v2.0"
}
},
"maturityAttributes": {
"productionStatus": "DEV"
},
"securityAttributes": {
"defaultGranularity": "boolean",
"securityLevels": [
"PUBLIC",
"REGISTERED",
"CONTROLLED"
]
}
}
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 1c52ad2b8fdde644939fe995a0b41d605b149502 | 2023-06-13T09:09:26 | framework/json/requests/filteringTerms.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"definitions": {
"AlphanumericFilter": {
"description": "Filter results based on operators and values applied to alphanumeric fields.",
"properties": {
"id": {
"description": "Field identfier to be queried.",
"example": "ageOfOnset",
"type": "string"
},
"operator": {
"default": "=",
"description": "Defines how the value relates to the field `id`.",
"enum": [
"=",
"<",
">",
"!",
">=",
"<="
],
"example": ">",
"type": "string"
},
"scope": {
"description": "The entry type to which the filter applies",
"example": "individuals",
"type": "string"
},
"value": {
"description": "Alphanumeric search term to be used within the query which can contain wildcard characters (%) to denote any number of unknown characters. Values can be assocatied with units if applicable.",
"example": "P70Y",
"type": "string"
}
},
"required": [
"id",
"operator",
"value"
],
"type": "object"
},
"CustomFilter": {
"description": "Filter results to include records that contain a custom term defined by this Beacon.",
"properties": {
"id": {
"description": "Custom filter terms should contain a unique identifier.",
"example": "demographic.ethnicity:asian",
"type": "string"
},
"scope": {
"description": "The entry type to which the filter applies",
"example": "individuals",
"type": "string"
}
},
"required": [
"id"
],
"type": "object"
},
"FilteringTerm": {
"anyOf": [
{
"$ref": "#/definitions/OntologyFilter"
},
{
"$ref": "#/definitions/AlphanumericFilter"
},
{
"$ref": "#/definitions/CustomFilter"
}
]
},
"OntologyFilter": {
"description": "Filter results to include records that contain a specific ontology term.",
"properties": {
"id": {
"description": "Term ID to be queried, using CURIE syntax where possible.",
"example": "HP:0002664",
"type": "string"
},
"includeDescendantTerms": {
"default": true,
"description": "Define if the Beacon should implement the ontology hierarchy, thus query the descendant terms of `id`.",
"type": "boolean"
},
"scope": {
"description": "The entry type to which the filter applies",
"example": "biosamples",
"type": "string"
},
"similarity": {
"default": "exact",
"description": "Allow the Beacon to return results which do not match the filter exactly, but do match to a certain degree of similarity. The Beacon defines the semantic similarity model implemented and how to apply the thresholds of 'high', 'medium' and 'low' similarity.",
"enum": [
"exact",
"high",
"medium",
"low"
],
"type": "string"
}
},
"required": [
"id"
],
"type": "object"
}
},
"description": "Filtering terms are the main means to select subsets of records from a Beacon response. While the name implies the application to a generated response, in practice implementations may apply them at the query stage. Note: In the processing of Beacon v2.0 requests multiple filters are assumed to be chained by the logical AND operator.",
"items": {
"$ref": "#/definitions/FilteringTerm"
},
"title": "Filtering Term Element",
"type": "array"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 1c03b708fdfd3e822886f51f0bb20f658030f76c | 2022-03-28T12:54:26 | models/json/beacon-v2-default-model/cohorts/examples/cohorts-MID-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"cohortDataTypes": [
{
"id": "OGMS:0000015",
"label": "clinical history"
},
{
"id": "OBI:0000070",
"label": "genotyping assay"
},
{
"id": "OMIABIS:0000060",
"label": "survey data"
}
],
"cohortDesign": {
"id": "OMIABIS:0001019",
"label": "longitudinal study design"
},
"cohortSize": 20000,
"cohortType": "study-defined",
"id": "cohort0001",
"inclusionCriteria": {
"ageRange": {
"end": {
"iso8601duration": "P40Y"
},
"start": {
"iso8601duration": "P18Y"
}
},
"genders": [
{
"id": "NCIT:C16576",
"label": "female"
},
{
"id": "NCIT:C20197",
"label": "male"
}
],
"locations": [
{
"id": "GAZ:00004501",
"label": "Catalonia Autonomous Community"
}
]
},
"name": "GCAT Genomes for Life"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | bc8f02a6a388140c854f3e17da3ccb779f2cbc0b | 2022-08-22T09:50:37 | framework/json/responses/sections/beaconReceivedRequestSummary.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "Section of the response that summarize the request received as it has been interpreted by the Beacon server. This summary can help to identify differences between the incoming request and its interpretation or processing, e.g. in the response granularity or pagination. The required properties include those that should be part of every request.",
"properties": {
"apiVersion": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/ApiVersion",
"description": "API version expected by the client to be supported by the server and used in the response format."
},
"filters": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/Filters",
"description": "Filters as submitted in the request."
},
"includeResultsetResponses": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/IncludeResultsetResponses"
},
"pagination": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/Pagination",
"description": "Pagination as requested for the results."
},
"requestParameters": {
"$ref": "../../requests/requestParameters.json",
"description": "Dictionary of request parameters received in the `RequestBody` or as part of a GET request."
},
"requestedGranularity": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/Granularity",
"description": "Requested granularity for the response which may differe from the response's actual granularity."
},
"requestedSchemas": {
"$comment": "TODO: Add the format attribute as a uri.",
"$ref": "../../common/beaconCommonComponents.json#/definitions/ListOfSchemas",
"description": "Set of schemas to be used in the response to a request. `minItems: 0` is used to confirm that an empty array is acceptable here.",
"minItems": 0
},
"testMode": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/TestMode",
"description": "Used for indicating that a request was received in a test context."
}
},
"required": [
"apiVersion",
"requestedSchemas",
"pagination",
"requestedGranularity"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 3e6093cf1b20ac74bc021c315511094f930be1ef | 2022-02-22T11:21:39 | framework/json/configuration/examples/entryTypeDefinition-MIN-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"defaultSchema": {
"id": "bdfGenericEntryType-v2",
"name": "Beacon v2 default schema for a basic element.",
"referenceToSchemaDefinition": "https://raw.githubusercontent.com/ga4gh-beacon/specification-v2-default-schemas/master/default_dataset_schema.yaml"
},
"id": "individual",
"name": "Individual entry",
"ontologyTermForThisType": {
"id": "DUO:0000004",
"label": "General Research Use"
},
"partOfSpecification": "Beacon v2"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 89f9aacffcb00b3395ffa9d908cf38c7bb598b5e | 2022-03-23T07:55:42 | models/json/beacon-v2-default-model/common/phenotypicFeature.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"definitions": {},
"description": "Used to describe a phenotype that characterizes the subject or biosample.",
"properties": {
"evidence": {
"$ref": "./evidence.json",
"description": "The evidence for an assertion of the observation of a type. RECOMMENDED."
},
"excluded": {
"default": false,
"description": "(from Phenopackets v.2) Flag to indicate whether the disease was observed or not. Default is \u2018false\u2019, in other words the disease was observed. Therefore it is only required in cases to indicate that the disease was looked for, but found to be absent. More formally, this modifier indicates the logical negation of the OntologyClass used in the 'featureType' field. CAUTION It is imperative to check this field for correct interpretation of the disease!",
"type": "boolean"
},
"featureType": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json",
"description": "Term denoting the phenotypic feature, preferably using a value from Human Phenotype Ontology (HPO)",
"examples": [
{
"id": "HP:0000002",
"label": "Abnormality of body height"
},
{
"id": "HP:0002006",
"label": "Facial cleft"
},
{
"id": "HP:0012469",
"label": "Infantile spasms"
}
]
},
"modifiers": {
"description": "For instance one or more terms from HPO Clinical Modifier (HP:0012823). This subontology is designed to provide terms to characterize and specify the phenotypic abnormalities defined in the Phenotypic abnormality subontology, with respect to severity, laterality, age of onset, and other aspects. [ HPO:probinson ] ",
"examples": [
{
"id": "HP:0032500",
"label": "Exacerbated by tobacco use"
},
{
"id": "HP:4000053",
"label": "Displaced fracture"
}
],
"items": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json"
},
"type": "array"
},
"notes": {
"description": "Unstructured text to describe additional properties of this phenotypic feature.",
"example": "Some free text",
"type": "string"
},
"onset": {
"$ref": "./timeElement.json",
"description": "Age or time at which the feature was first observed."
},
"resolution": {
"$ref": "./timeElement.json",
"description": "Age or time at which the feature resolved or abated."
},
"severityLevel": {
"$ref": "./commonDefinitions.json#/definitions/SeverityLevel"
}
},
"required": [
"featureType"
],
"title": "PhenotypicFeature",
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 030747a0ef492bd79dc53d3eaf9f6c16ceae236a | 2022-02-22T13:50:28 | framework/json/requests/examples-fullDocuments/beaconRequestBody-MAX-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"meta": {
"apiVersion": "2.0",
"requestedSchemas": [
{
"entityType": "EntryTypeA",
"schema": "entry-typeA-schema-v0.1"
}
]
},
"query": {
"filters": [
{
"id": "EFO:0001212",
"scope": "biosamples"
}
],
"includeResultsetResponses": "HIT",
"pagination": {
"limit": 10,
"skip": 0
},
"requestParameters": {
"datasets": {
"datasetIds": [
"DatasetXYZ",
"Dataset123"
]
}
},
"requestedGranularity": "boolean",
"testMode": false
}
} | CC0-1.0 | en |
Subsets and Splits