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ga4gh-beacon/beacon-v2 | 86d8c3bebb92dc892e2560022884e1ddea491821 | 2022-02-22T13:58:39 | framework/json/responses/examples-fullDocuments/beaconFilteringTermsResponse-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"info": {},
"meta": {
"apiVersion": "string",
"beaconId": "string",
"returnedSchemas": [
{
"map": "beacon-map-v2.0.0"
}
]
},
"response": {
"filteringTerms": [
{
"id": "PATO:0000011",
"label": "age",
"type": "numeric"
},
{
"id": "HP:0008773",
"label": "Aplasia/Hypoplasia of the middle ear",
"type": "Human Phenotype Ontology"
},
{
"id": "ownsIPhone",
"label": "Individuals associated with this term owns an IPhone",
"type": "custom"
}
],
"resources": [
{
"id": "hp",
"iriPrefix": "http://purl.obolibrary.org/obo/HP_",
"name": "Human Phenotype Ontology",
"namespacePrefix": "HP",
"url": "http://purl.obolibrary.org/obo/hp.owl",
"version": "27-03-2020"
}
]
}
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 030747a0ef492bd79dc53d3eaf9f6c16ceae236a | 2022-02-22T13:50:28 | framework/json/responses/sections/beaconBooleanResponseSection.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "Boolean (true/false) response section.",
"properties": {
"exists": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/Exists",
"description": "Indicator of whether any entry was observed. This should be non-null, unless there was an error, in which case an error response is expected instead of this one."
}
},
"required": [
"exists"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 89ed443fecde703f259d5ec169ceeede37db72f9 | 2022-03-09T07:58:30 | models/json/beacon-v2-default-model/biosamples/filteringTerms.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"filteringTerms": []
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 89f9aacffcb00b3395ffa9d908cf38c7bb598b5e | 2022-03-23T07:55:42 | models/json/beacon-v2-default-model/common/evidence.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"description": "Definition of an evidence class. Provenance: GA4GH Phenopackets v2 `Evidence`",
"properties": {
"evidenceCode": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json",
"description": "An ontology class that represents the evidence type",
"example": {
"id": "ECO:0006017",
"label": "author statement from published clinical study used in manual assertion"
}
},
"reference": {
"$ref": "./externalReference.json",
"description": "Representation of the source of the evidence",
"example": {
"id": "PMID:30962759",
"label": "Recurrent Erythema Nodosum in a Child with a SHOC2 Gene Mutation"
}
}
},
"required": [
"evidenceCode"
],
"title": "Evidence",
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | f3f93ef9f94f0164a185d36dd45045fc1a179c14 | 2022-12-21T19:45:33 | framework/json/responses/sections/beaconFilteringTermsResults.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$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": [
"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 | 89f9aacffcb00b3395ffa9d908cf38c7bb598b5e | 2022-03-23T07:55:42 | framework/json/responses/beaconEntryTypesResponse.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"description": "Response including a list of Entry types definitions.",
"properties": {
"meta": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/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": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/configuration/entryTypesSchema.json",
"description": "Returning the Beacon Entry Types."
}
},
"required": [
"meta",
"response"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | f3f93ef9f94f0164a185d36dd45045fc1a179c14 | 2022-12-21T19:45:33 | framework/json/responses/beaconFilteringTermsResponse.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$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": {
"$ref": "./sections/beaconInformationalResponseMeta.json"
},
"response": {
"$ref": "./sections/beaconFilteringTermsResults.json"
}
},
"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/examples/cohorts-MAX-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"cohortDataTypes": [
{
"id": "OGMS:0000015",
"label": "clinical history"
},
{
"id": "OBI:0000070",
"label": "genotyping assay"
},
{
"id": "OMIABIS:0000060",
"label": "survey data"
}
],
"cohortDesign": {
"id": "OMIABIS:0001019",
"label": "longitudinal study design"
},
"cohortId": "cohort0001",
"cohortInclusionCriteria": {
"ageRange": {
"end": {
"iso8601duration": "P40Y"
},
"start": {
"iso8601duration": "P18Y"
}
},
"genders": [
{
"id": "NCIT:C16576",
"label": "female"
},
{
"id": "NCIT:C20197",
"label": "male"
}
],
"locations": [
{
"id": "GAZ:00004501",
"label": "Catalonia Autonomous Community"
}
]
},
"cohortName": "GCAT Genomes for Life",
"cohortSize": 20000,
"cohortType": "study-defined",
"collectionEvents": [
{
"eventDataTypes": {
"availability": true,
"distribution": {
"dataTypes": {
"blood collected from fasting subject": 51,
"survey data": 98
}
}
},
"eventDate": "2019-04-23",
"eventEthnicities": {
"availability": true,
"availabilityCount": 101,
"distribution": {
"ethnicities": {
"African": 3,
"European": 90,
"Latin American": 8
}
}
},
"eventGenders": {
"availability": true,
"availabilityCount": 101,
"distribution": {
"genders": {
"female": 51,
"male": 50
}
}
},
"eventNum": 1,
"eventSize": 101
}
]
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 565e45856add68e73cab902635f1632bf9b40bb1 | 2022-12-22T09:27:04 | framework/json/requests/requestParameters.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": {
"type": "object"
},
"description": "The schema below is a placeholder for a dictionary 'key':'object'. The individual definitions depend on the model (e.g. beacon-v2-default-model) and entity (e.g. `genomicVariant`).",
"properties": {
"$schema": {
"description": "Added here to allow proper validation of the documents w/o providing specific values.",
"type": "string"
}
},
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | f3f93ef9f94f0164a185d36dd45045fc1a179c14 | 2022-12-21T19:45:33 | framework/json/responses/sections/beaconBooleanResponseSection.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "Boolean (true/false) response section.",
"properties": {
"exists": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/Exists"
}
},
"required": [
"exists"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 89f9aacffcb00b3395ffa9d908cf38c7bb598b5e | 2022-03-23T07:55:42 | framework/json/responses/beaconConfigurationResponse.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$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": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/sections/beaconInformationalResponseMeta.json",
"description": "Information about the response that could be relevant for the Beacon client in order to interpret the results."
},
"response": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/configuration/beaconConfigurationSchema.json",
"description": "Returning the Beacon configuration."
}
},
"required": [
"meta",
"response"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 7b0d8d88af4dbea3a9e96598247ef89fad716782 | 2022-09-09T08:49:12 | 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": [
{
"ageGroup": {
"id": "NCIT:C49685",
"label": "Adult 18-65 Years Old"
}
},
{
"age": {
"iso8601duration": "P32Y6M1D"
}
},
{
"ageRange": {
"end": {
"iso8601duration": "P59Y"
},
"start": {
"iso8601duration": "P18Y"
}
}
},
{
"age": {
"iso8601duration": "P2M4D"
}
}
]
},
"diseaseCode": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json",
"description": "Disease identifier. Value from disease ontologies such as HPO, OMIM, Orphanet, MONDO, e.g. lactose intolerance (HP:0004789, ICD10CM:E73). Provenance: GA4GH Phenopackets v2 `Disease.term`",
"examples": [
{
"id": "HP:0004789",
"label": "lactose intolerance"
},
{
"id": "ICD10CM:E73",
"label": "lactose intolerance"
},
{
"id": "OMIM:164400",
"label": "Spinocerebellar ataxia 1"
}
]
},
"familyHistory": {
"description": "Boolean indicating determined or self-reported presence of family history of the disease.",
"examples": [
true
],
"type": "boolean"
},
"notes": {
"description": "Unstructured text to describe additional properties of this disease instance.",
"examples": [
"Some free text"
],
"type": "string"
},
"severity": {
"$ref": "./commonDefinitions.json#/definitions/SeverityLevel",
"examples": [
{
"id": "HP:0012828",
"label": "Severe"
},
{
"id": "HP:0012826",
"label": "Moderate"
}
]
},
"stage": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json",
"description": "Ontology term from Ontology for General Medical Science (OGMS), e.g. acute onset (OGMS:0000119). Provenance: GA4GH Phenopackets v2 `Disease.disease_stage`",
"examples": [
{
"id": "OGMS:0000119",
"label": "acute onset"
},
{
"id": "OGMS:0000117",
"label": "asymptomatic"
},
{
"id": "OGMS:0000106",
"label": "remission"
}
]
}
},
"required": [
"diseaseCode"
],
"title": "Disease",
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 60904b990df006b581ad41b9562360edb97402c4 | 2022-03-23T10:10:35 | models/json/beacon-v2-default-model/genomicVariations/examples/genomicVariant-MID-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$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"
}
]
},
"position": {
"assemblyId": "GRCh38",
"refseqId": "chr1",
"start": [
55039979
]
},
"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"
},
"sequenceId": "refseq:NC_000001.11",
"type": "SequenceLocation"
},
"referenceBases": "G",
"variantType": "SNP"
}
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 3e6093cf1b20ac74bc021c315511094f930be1ef | 2022-02-22T11:21:39 | framework/json/responses/beaconBooleanResponse.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "Complete definition for a minimal response that does *only* a `boolean` exists true|false answer.",
"properties": {
"beaconHandovers": {
"$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": {
"$ref": "./sections/beaconBooleanResponseSection.json",
"description": "Boolean (true/false) response section."
}
},
"required": [
"meta",
"responseSummary"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 2a2b786e4a1845ea23d71dfe8125957b6f3d742f | 2022-06-20T13:19:32 | framework/json/responses/beaconMapResponse.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$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/beaconMapSchema.json",
"description": "Returning the Beacon Map."
}
},
"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/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"
},
{
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-unity-testing/main/framework/json/common/ontologyTerm.json"
}
],
"title": "Value",
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 519aa575490d2c1b453efd588492b8ce770591b7 | 2022-07-22T12:06:39 | models/json/beacon-v2-default-model/common/exposure.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"description": "Exposures (lifestyle, behavioural exposures) occurred to individual, defined by exposure ID, date and age of onset, dose, and duration.",
"properties": {
"ageAtExposure": {
"$ref": "../common/age.json"
},
"date": {
"description": "Date of the exposure in ISO8601 format.",
"format": "date",
"type": "string"
},
"duration": {
"description": "Exposure duration in ISO8601 format",
"examples": [
"P2Y6M1D"
],
"type": "string"
},
"exposureCode": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json",
"description": "Exposure ID. Recommended is a value from Environment Exposure Ontology.",
"examples": [
{
"id": "CHEBI:46661",
"label": "asbestos"
},
{
"id": "ENVO:21001217",
"label": "X-ray radiation"
}
]
},
"unit": {
"$ref": "../common/commonDefinitions.json#/definitions/Unit",
"description": "Unit of the exposure. Recommended from NCIT Unit of Category ontology term (NCIT:C42568) descendants."
},
"value": {
"description": "Quantification of the exposure.",
"type": "number"
}
},
"required": [
"exposureCode",
"ageAtExposure",
"unit",
"duration"
],
"title": "Exposure",
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 86d8c3bebb92dc892e2560022884e1ddea491821 | 2022-02-22T13:58:39 | framework/json/responses/examples-fullDocuments/beaconEntryTypesResponse-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$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": {
"$schema": "../../configuration/entryTypesSchema.json",
"entryTypes": {
"dataset": {
"aCollectionOf": [
{
"id": "exampleEntry",
"name": "Example entries"
}
],
"additionallySupportedSchemas": [],
"defaultSchema": {
"id": "datasetDefaultSchema",
"name": "Default schema for datasets",
"referenceToSchemaDefinition": "./datasets/defaultSchema.json",
"schemaVersion": "v.2"
},
"description": "A Dataset is a collection of records, like rows in a database or cards in a cardholder.",
"endpoint": "/datasets",
"filteringTermsReference": "./datasets/filteringTerms.json",
"id": "dataset",
"name": "Dataset",
"ontologyTermForThisType": {
"id": "NCIT:C47824",
"label": "Data set"
},
"partOfSpecification": "Beacon v2.0"
},
"exampleEntry": {
"additionallySupportedSchemas": [],
"defaultSchema": {
"id": "ExampleEntryTypeDefaultschema",
"name": "Default schema for an example entries",
"referenceToSchemaDefinition": "./exampleEntry/defaultSchema.json",
"schemaVersion": "v.2"
},
"description": "A generic entry type to allow testing and playing with the specification.",
"endpoint": "./exampleEntries",
"filteringTermsReference": "./exampleEntry/filteringTerms.json",
"id": "exampleEntry",
"name": "Example Entry",
"ontologyTermForThisType": {
"id": "NCIT:C20181",
"label": "Conceptual Entity"
},
"partOfSpecification": "Beacon v2.0"
}
}
}
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 89ed443fecde703f259d5ec169ceeede37db72f9 | 2022-03-09T07:58:30 | models/json/beacon-v2-default-model/common/referenceRange.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"description": "Definition of a range class.",
"properties": {
"high": {
"description": "Upper range end of normal",
"examples": [
135
],
"type": "number"
},
"low": {
"description": "Lower range end of normal",
"examples": [
85
],
"type": "number"
},
"unit": {
"$ref": "./commonDefinitions.json#/definitions/Unit",
"description": "The kind of unit. RECOMMENDED.",
"examples": [
{
"id": "NCIT:C49670",
"label": "Millimeter of Mercury"
}
]
}
},
"required": [
"low",
"high"
],
"title": "ReferenceRange",
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 030747a0ef492bd79dc53d3eaf9f6c16ceae236a | 2022-02-22T13:50:28 | framework/json/responses/examples-sections/beaconInformationalResponseMeta-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"apiVersion": "v2.0",
"beaconId": "org.examplebeacons.beacon-v2",
"returnedSchemas": []
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 030747a0ef492bd79dc53d3eaf9f6c16ceae236a | 2022-02-22T13:50:28 | 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": "Rules for selecting records based upon the field values those records contain. Filters are separated 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 | bf2d78821c80404be777c9f0df35f79e8424bbd6 | 2022-03-24T08:35:39 | 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."
},
"severity": {
"$ref": "./commonDefinitions.json#/definitions/SeverityLevel",
"examples": [
{
"id": "HP:0012828",
"label": "Severe"
},
{
"id": "HP:0012826",
"label": "Moderate"
}
]
}
},
"required": [
"featureType"
],
"title": "PhenotypicFeature",
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 030747a0ef492bd79dc53d3eaf9f6c16ceae236a | 2022-02-22T13:50:28 | framework/json/responses/examples-sections/beaconResultsets-MAX-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"resultSets": [
{
"exists": false,
"id": "datasetA",
"type": "dataset"
},
{
"exists": true,
"id": "datasetB",
"results": [
{
"id": "BEex3",
"name": "Basic Element example three"
},
{
"id": "BEex4",
"name": "Basic Element example four"
}
],
"resultsCount": 2,
"resultsHandovers": [
{
"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"
}
],
"type": "dataset"
}
]
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 030747a0ef492bd79dc53d3eaf9f6c16ceae236a | 2022-02-22T13:50:28 | 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. 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. - `boolean`: returns 'true/false' responses.\n\n - `count`: adds the total number of positive results found.\n\n - `aggregated`: returns summary, aggregated or distribution like responses.\n\n. - `record`: returns details for every row. The cases where a Beacon prefers to return records with less, not all attributes, different strategies have been considered, e.g.: keep non-mandatory attributes empty, or Beacon to provide a minimal record definition, but these strategies still need to be tested in real world cases and hence no design decision has been taken yet.",
"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.: a link to a request access page, or to a temporarily saved detailed response, which can include a temporary token.",
"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 RFC\n3986 format).",
"example": "https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0/",
"format": "uri",
"type": "string"
}
},
"required": [
"handoverType",
"url"
],
"type": "object"
},
"HandoverType": {
"description": "Handover type, as an Ontology_term object with CURIE syntax for the\n`id` value.",
"properties": {
"id": {
"default": "CUSTOM",
"description": "Use `CUSTOM` for the `id` when no ontology is available.",
"example": "EFO:0004157",
"type": "string"
},
"label": {
"default": null,
"description": "This would be the \"preferred Label\" in the case of an ontology term.",
"example": "BAM format",
"type": "string"
}
},
"required": [
"id"
],
"type": "object"
},
"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.\n\nUse `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": {
"$comment": "TO DO: Add the correct format as 'uri' or 'regex'",
"examples": [
"./ga4gh-beacon-dataset-v2.0.0",
"https://www.example.org/schemas/ga4gh-beacon-dataset-v2.0.0.json"
],
"type": "string"
}
},
"type": "object"
},
"Skip": {
"default": 0,
"description": "In the request: number of pages to skip.\n In the response: number of pages that has been skipped.",
"example": 0,
"minimum": 0,
"type": "integer"
},
"TestMode": {
"default": false,
"description": "Used for indicating that a request or response is done in a test context. Purposed for compliance testing. It DOES NOT mean that the Beacon instance is a test instance, but that this specific request-response cycle is a testing one. When 'true' the Beacon instance MUST respond the request but it SHOULD use fake or non-sensitive data or content as what is being evaluated is the acceptance/understanding of a request and the structure of the returned response by the Beacon instance.",
"type": "boolean"
}
},
"description": "Definition of relatively simple components used in different points of the Beacon specification, both in requests and responses, therefore not associated exclusively with one or the other.\n If a component is complex a separated schema is provided.",
"title": "Beacon Common Components",
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 3e6093cf1b20ac74bc021c315511094f930be1ef | 2022-02-22T11:21:39 | framework/json/responses/beaconConfigurationResponse.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$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 | 9eaada7ca0410f4127d0c324880033e60024d128 | 2022-03-13T12:14:16 | models/json/beacon-v2-default-model/runs/filteringTerms.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"filteringTerms": []
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 86d8c3bebb92dc892e2560022884e1ddea491821 | 2022-02-22T13:58:39 | framework/json/requests/examples-sections/filteringTerms-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"filters": [
{
"id": "HP:0002664",
"includeDescendantTerms": true,
"scope": "biosamples",
"similarity": "exact"
},
{
"id": "age",
"operator": ">=",
"scope": "individuals",
"value": "P70Y"
},
{
"id": "demographic.ethnicity:asian",
"scope": "cohorts"
}
]
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 89ed443fecde703f259d5ec169ceeede37db72f9 | 2022-03-09T07:58:30 | models/json/beacon-v2-default-model/genomicVariations/requestParametersComponents.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"definitions": {
"AlternateBases": {
"description": "Alternate bases for this variant (starting from `start`).\n* Accepted values: [ACGTN]*.\n* N is a wildcard, that denotes the position of any base, and can be\nused as a standalone base of any type or within a partially known\nsequence. As example, a query of `ANNT` the Ns can take take any form of\n[ACGT] and will match `ANNT`, `ACNT`, `ACCT`, `ACGT` ... and so forth.\n* an *empty value* is used in the case of deletions with the maximally\ntrimmed, deleted sequence being indicated in `ReferenceBases`\n* Categorical variant queries, e.g. such *not* being represented through\nsequence & position, make use of the `variantType` parameter.\n* either `alternateBases` or `variantType` is required.",
"pattern": "^([ACGTUNRYSWKMBDHV\\-\\.]*)$",
"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, and can be used as a standalone base of any type or within a partially known sequence. As example, a query of `ANNT` the Ns can take take any form of [ACGT] and will match `ANNT`, `ACNT`, `ACCT`, `ACGT` ... and so forth. * an *empty value* is used in the case of insertions with the maximally trimmed, inserted sequence being indicated in `AlternateBases`",
"pattern": "^([ACGTUNRYSWKMBDHV\\-\\.]*)$",
"type": "string"
}
},
"description": "Component definitions used in 'requestParameters.json'.\nThe purpose of this file is to separate components from actual parameters to avoid confusion."
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | bf2d78821c80404be777c9f0df35f79e8424bbd6 | 2022-03-24T08:35:39 | models/json/beacon-v2-default-model/individuals/examples/individual-with-pedigree-MID-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$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,
"severity": {
"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 | 86d8c3bebb92dc892e2560022884e1ddea491821 | 2022-02-22T13:58:39 | 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": {
"$ref": "#/definitions/Resource"
},
"type": "array"
}
},
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 030747a0ef492bd79dc53d3eaf9f6c16ceae236a | 2022-02-22T13:50:28 | framework/json/responses/examples-fullDocuments/beaconCollectionsResponse-MIN-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$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": "dataset",
"schema": "dataset-schema-v1.0"
}
]
},
"returnedSchemas": [
{
"entityType": "dataset",
"schema": "dataset-schema-v1.0"
}
]
},
"response": {
"collections": []
},
"responseSummary": {
"exists": true
}
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 3e6093cf1b20ac74bc021c315511094f930be1ef | 2022-02-22T11:21:39 | 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": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/NumTotalResults",
"description": "Total number of results."
}
},
"required": [
"exists",
"numTotalResults"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 86d8c3bebb92dc892e2560022884e1ddea491821 | 2022-02-22T13:58:39 | framework/json/configuration/examples/entriesCollectionDefinition_MIN_example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"aCollectionOf": [
{
"id": "exampleEntry",
"name": "Example entries"
}
],
"defaultSchema": {
"id": "datasetDefaultSchema",
"name": "Default schema for datasets",
"referenceToSchemaDefinition": "./datasets/defaultSchema.json",
"schemaVersion": "v.2"
},
"id": "dataset",
"name": "Dataset",
"ontologyTermForThisType": {
"id": "NCIT:C47824",
"label": "Data set"
},
"partOfSpecification": "Beacon v2.0"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 030747a0ef492bd79dc53d3eaf9f6c16ceae236a | 2022-02-22T13:50:28 | framework/json/responses/beaconEntryTypesResponse.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"description": "Response including a list of Entry types definitions.",
"properties": {
"meta": {
"$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": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-unity/main/framework/json/configuration/entryTypesSchema.json",
"description": "Returning the Beacon Entry Types."
}
},
"required": [
"meta",
"response"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 030747a0ef492bd79dc53d3eaf9f6c16ceae236a | 2022-02-22T13:50:28 | framework/json/responses/beaconMapResponse.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$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/beaconMapSchema.json",
"description": "Returning the Beacon Map."
}
},
"required": [
"meta",
"response"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 284e82aa022ef5eccc996d957e3af4fbf261c8c8 | 2022-02-24T11:37:28 | 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-testing/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": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-unity-testing/main/framework/json/configuration/beaconConfigurationSchema.json",
"description": "Returning the Beacon configuration."
}
},
"required": [
"meta",
"response"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 8e09eabe19cfa57526eefd1765154ec2c985eede | 2022-10-11T11:03:58 | framework/json/responses/beaconCountResponse.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "Complete definition for a response that does not include record level details but provides `Boolean` and `count` information.",
"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/beaconCountResponseSection.json",
"description": "Response summary, including Boolean and optionally results count."
}
},
"required": [
"meta",
"responseSummary"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 2c53ba10fba1bf39152e286d3a6edc756de7f6fc | 2022-04-05T15:50:47 | models/json/beacon-v2-default-model/genomicVariations/examples/genomicVariant-MIN-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"variantInternalId": "GRCh37-1-55505652-G-A",
"variation": {
"alternateBases": "A",
"location": {
"interval": {
"end": {
"type": "Number",
"value": 5505653
},
"start": {
"type": "Number",
"value": 5505652
},
"type": "SequenceInterval"
},
"sequence_id": "refseq:NC_000001.10",
"type": "SequenceLocation"
},
"variantType": "SNP"
}
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 89ed443fecde703f259d5ec169ceeede37db72f9 | 2022-03-09T07:58:30 | models/json/beacon-v2-default-model/datasets/examples/dataset-MIN-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"id": "ds01010101",
"name": "Dataset with synthetic data"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 030747a0ef492bd79dc53d3eaf9f6c16ceae236a | 2022-02-22T13:50:28 | framework/json/responses/examples-fullDocuments/beaconMapResponse-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": "../../configuration/beaconMapSchema.json",
"endpointSets": {
"dataset": {
"endpoints": {
"exampleEntries": {
"returnedEntryType": "exampleEntry",
"url": "https://exampleBeacons.org/datasets/{id}/exampleEntries"
}
},
"entryType": "dataset",
"filteringTermsUrl": "https://exampleBeacons.org/datasets/{id}/filteringTerms",
"openAPIEndpointsDefinition": "./datasets/endpoints.json",
"rootUrl": "https://exampleBeacons.org/datasets",
"singleEntryUrl": "https://exampleBeacons.org/datasets/{id}"
},
"exampleEntry": {
"entryType": "exampleEntry",
"filteringTermsUrl": "https://exampleBeacons.org/exampleEntries/{id}/filteringTerms",
"openAPIEndpointsDefinition": "./exampleEntries/endpoints.json",
"rootUrl": "https://exampleBeacons.org/exampleEntries",
"singleEntryUrl": "https://exampleBeacons.org/exampleEntries/{id}"
}
}
}
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 89ed443fecde703f259d5ec169ceeede37db72f9 | 2022-03-09T07:58:30 | models/json/beacon-v2-default-model/common/externalReference.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"description": "Definition of an external reference class. Provenance: GA4GH Phenopackets v2 `ExternalReference`",
"properties": {
"id": {
"description": "An application specific identifier. RECOMMENDED.",
"example": "PMID:34054918",
"type": "string"
},
"notes": {
"description": "An optional text descriptor. Renamed compared to GA4GH Phenopackets v2 `ExternalReference.description`",
"example": "Signatures of Discriminative Copy Number Aberrations in 31 Cancer Subtypes",
"type": "string"
},
"reference": {
"description": "A url.",
"example": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8155688/",
"type": "string"
}
},
"required": [],
"title": "ExternalReference",
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | db307ba9b47b47664daf441fb28fbbe6ac913096 | 2024-03-21T14:20:16 | framework/json/responses/sections/beaconFilteringTermsResults.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$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": [
"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 | 89ed443fecde703f259d5ec169ceeede37db72f9 | 2022-03-09T07:58:30 | models/json/beacon-v2-default-model/common/pedigree.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"definitions": {
"pedigreeMember": {
"examples": [
{
"membersInProband": [
{
"affected": true,
"memberId": "Ind0012122",
"role": {
"id": "NCIT:C64435",
"label": "Proband"
}
},
{
"affected": false,
"memberId": "Pedigree1001-m2",
"role": {
"id": "NCIT:C96580",
"label": "Biological Mother"
}
},
{
"affected": true,
"memberId": "Pedigree1001-m3",
"role": {
"id": "NCIT:C96572",
"label": "Biological Father"
}
}
]
},
{
"membersInMother": [
{
"affected": false,
"memberId": "Ind0028989",
"role": {
"id": "NCIT:C96580",
"label": "Biological Mother"
}
},
{
"affected": true,
"memberId": "Ind0012122",
"role": {
"id": "NCIT:C64435",
"label": "Proband"
}
}
]
}
],
"properties": {
"affected": {
"description": "Is the individual affected by the disease in the pedigree?",
"type": "boolean"
},
"memberId": {
"description": "Identifier of the individual. The individual could be part of the same Beacon datasets or not, in which case the information here is meant to complete the pedigree. If the individual is also in the dataset use that Individual ID. If it is not the in the dataset, use a non-collading ID, e.g. concatenating the Pedigree ID with a local ID, similarly to the example 'Pedigree1001-m1'.",
"examples": [
"Pedigree1001-m1",
"Ind0012122"
],
"type": "string"
},
"role": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-unity-testing/main/framework/json/common/ontologyTerm.json",
"description": "Pedigree role, defined as relationship to proband. Value from Family Member term (NCIT:C41256), e.g. \"proband\" (NCIT:C64435),\"identical twin\" (NCIT:C73429), \"mother\" (NCIT:C25189).",
"examples": [
{
"id": "NCIT:C64435",
"label": "Proband"
},
{
"id": "NCIT:C96580",
"label": "Biological Mother"
},
{
"id": "NCIT:C96572",
"label": "Biological Father"
},
{
"id": "NCIT:C165848",
"label": "Identical Twin Brother"
}
]
}
},
"required": [
"memberId",
"role",
"affected"
],
"type": "object"
}
},
"description": "Pedigree studies in which the individual is part of.",
"properties": {
"disease": {
"$ref": "../common/disease.json"
},
"id": {
"description": "Pedigree identifier.",
"example": "Pedigree1001",
"type": "string"
},
"members": {
"description": "List of members of the pedigree. If the current pedigree definition is attached to the proband, it contains the whole list of pedigree members, including the proband. If the definition is attached to an individual different than the proband, it only contains two entries: one that describes that member, e.g. the proband mother or father, and one that points to the proband.",
"items": {
"$ref": "#/definitions/pedigreeMember"
},
"minItems": 1,
"type": "array"
},
"numSubjects": {
"description": "Total number of subjects in pedigree.",
"example": 10,
"type": "integer"
}
},
"required": [
"id",
"disease",
"members"
],
"title": "Pedigree",
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 89f9aacffcb00b3395ffa9d908cf38c7bb598b5e | 2022-03-23T07:55:42 | models/json/beacon-v2-default-model/common/exposure.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"description": "Exposures (lifestyle, behavioural exposures) occurred to individual,defined by exposure ID, date and age of onset, dose, and duration.",
"properties": {
"ageAtExposure": {
"$ref": "../common/age.json"
},
"date": {
"description": "Date of the exposure in ISO8601 format.",
"format": "date",
"type": "string"
},
"duration": {
"description": "Exposure duration in ISO8601 format",
"example": "P32Y6M1D",
"type": "string"
},
"exposureCode": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json",
"description": "Exposure ID. Value from Environment Exposure Ontology.",
"examples": [
{
"id": "CHEBI:46661",
"label": "asbestos"
},
{
"id": "ENVO:21001217",
"label": "X-ray radiation"
}
]
},
"unit": {
"$ref": "../common/commonDefinitions.json#/definitions/Unit",
"description": "Unit of the exposure. Recommended from NCIT Unit of Category ontology term (NCIT:C42568) descendants."
},
"value": {
"description": "Quantification of the exposure.",
"type": "number"
}
},
"required": [
"exposureCode",
"ageAtExposure",
"units",
"duration"
],
"title": "Procedure",
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 030747a0ef492bd79dc53d3eaf9f6c16ceae236a | 2022-02-22T13:50:28 | framework/json/common/validation/beaconCommonComponents.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false,
"properties": {
"$schema": {
"description": "Added here to allow the example to comply with the 'additionalProperties:true' restriction.",
"type": "string"
},
"apiVersion": {
"$ref": "../beaconCommonComponents.json#/definitions/ApiVersion"
},
"beaconError": {
"$ref": "../beaconCommonComponents.json#/definitions/BeaconError"
},
"beaconId": {
"$ref": "../beaconCommonComponents.json#/definitions/BeaconId"
},
"exists": {
"$ref": "../beaconCommonComponents.json#/definitions/Exists"
},
"filters": {
"$ref": "../beaconCommonComponents.json#/definitions/Filters"
},
"handover": {
"$ref": "../beaconCommonComponents.json#/definitions/Handover"
},
"handoverType": {
"$ref": "../beaconCommonComponents.json#/definitions/HandoverType"
},
"includeResultsetResponses": {
"$ref": "../beaconCommonComponents.json#/definitions/IncludeResultsetResponses"
},
"info": {
"$ref": "../beaconCommonComponents.json#/definitions/Info"
},
"listOfHandovers": {
"$ref": "../beaconCommonComponents.json#/definitions/ListOfHandovers"
},
"listOfSchemas": {
"$ref": "../beaconCommonComponents.json#/definitions/ListOfSchemas"
},
"numTotalResults": {
"$ref": "../beaconCommonComponents.json#/definitions/NumTotalResults"
},
"pagination": {
"$ref": "../beaconCommonComponents.json#/definitions/Pagination"
},
"schemasPerEntity": {
"$ref": "../beaconCommonComponents.json#/definitions/SchemasPerEntity"
}
},
"title": "Schema for validating Beacon Common Components examples",
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | ffff90479120b6fd8753a1fdb6125b65cd2ac3b9 | 2022-03-21T07:59:58 | models/json/beacon-v2-default-model/common/referenceRange.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"description": "Definition of a range class.",
"properties": {
"high": {
"description": "Upper range end of normal",
"examples": [
135
],
"type": "number"
},
"low": {
"description": "Lower range end of normal",
"examples": [
85
],
"type": "number"
},
"unit": {
"$ref": "./commonDefinitions.json#/definitions/Unit",
"description": "The kind of unit.",
"examples": [
{
"id": "NCIT:C49670",
"label": "Millimeter of Mercury"
}
]
}
},
"required": [
"unit",
"low",
"high"
],
"title": "ReferenceRange",
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 86d8c3bebb92dc892e2560022884e1ddea491821 | 2022-02-22T13:58:39 | framework/json/responses/beaconBooleanResponse.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "Complete definition for a minimal response that does *only* a `boolean` exists true|false answer.",
"properties": {
"beaconHandovers": {
"$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": {
"$ref": "./sections/beaconBooleanResponseSection.json",
"description": "Boolean (true/false) response section."
}
},
"required": [
"meta",
"responseSummary"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 6ae39647913d2c7cc7f4320439e984f3951c3645 | 2022-03-23T09:13:35 | framework/json/responses/beaconCountResponse.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$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/beaconCountResponseSection.json",
"description": "Response summary, including Boolean and optionally results count."
}
},
"required": [
"meta",
"responseSummary"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | edf561ed1a4c612efd3921beecbb5f6378c684f2 | 2024-03-20T15:02:44 | 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\"]"
],
"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": {
"$ref": "#/definitions/Resource"
},
"type": "array"
}
},
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 5468efe2aeea4398e89c1321ae060ceba835571e | 2023-06-04T13:51:19 | framework/json/responses/examples-fullDocuments/beaconFilteringTermsResponse-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"info": {},
"meta": {
"apiVersion": "string",
"beaconId": "string",
"returnedSchemas": [
{
"map": "beacon-map-v2.0.0"
}
]
},
"response": {
"filteringTerms": [
{
"id": "PATO:0000011",
"label": "age",
"type": "numeric"
},
{
"id": "HP:0008773",
"label": "Aplasia/Hypoplasia of the middle ear",
"type": "Human Phenotype Ontology"
},
{
"id": "ownsIPhone",
"label": "Individuals associated with this term owns an IPhone",
"type": "custom"
}
],
"resources": [
{
"id": "hp",
"iriPrefix": "https://purl.obolibrary.org/obo/HP_",
"name": "Human Phenotype Ontology",
"namespacePrefix": "HP",
"url": "https://purl.obolibrary.org/obo/hp.owl",
"version": "27-03-2020"
}
]
}
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 3e6093cf1b20ac74bc021c315511094f930be1ef | 2022-02-22T11:21:39 | 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": {
"$ref": "./beaconRequestMeta.json",
"description": "Information that is relevant to build the response."
},
"query": {
"description": "Parameters to limit the list of returned results.",
"properties": {
"filters": {
"$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 to apply on the results."
},
"requestParameters": {
"$ref": "./requestParameters.json",
"description": "TBD"
},
"requestedGranularity": {
"$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."
},
"testMode": {
"$ref": "../common/beaconCommonComponents.json#/definitions/TestMode",
"description": "Used for indicating that a request or response is done in a test context. Purposed for compliance testing."
}
},
"type": "object"
}
},
"required": [
"meta"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 3e6093cf1b20ac74bc021c315511094f930be1ef | 2022-02-22T11:21:39 | framework/json/responses/examples-fullDocuments/beaconCollectionsResponse-MID-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$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": "dataset",
"schema": "dataset-schema-v1.0"
}
]
},
"returnedSchemas": [
{
"entityType": "dataset",
"schema": "dataset-schema-v1.0"
}
]
},
"response": {
"collections": [
{
"$schema": "https://schemas-fake-depot.org/beaconv2/datasetSchema.json",
"createDateTime": "2011-01-11T11:11:11Z",
"dataUseConditions": {
"duoDataUse": [
{
"id": "DUO:0000007",
"label": "disease specific research",
"modifiers": [
{
"id": "HP:0001631"
}
],
"version": "2021-02-23"
}
]
},
"description": "This is the first dataset",
"id": "Dataset1",
"name": "Dataset One",
"updateDateTime": "2011-01-11T11:11:11Z",
"version": "v1"
},
{
"$schema": "https://schemas-fake-depot.org/beaconv2/datasetSchema.json",
"createDateTime": "2012-02-22T22:22:22Z",
"dataUseConditions": {
"duoDataUse": [
{
"id": "DUO:0000042",
"label": "general research use",
"version": "2021-02-23"
}
]
},
"description": "This is the second dataset",
"id": "Dataset2",
"name": "Dataset Two",
"updateDateTime": "2012-02-22T22:22:22Z",
"version": "v2"
}
]
},
"responseSummary": {
"exists": true
}
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | a7526f5377ad2d909eca551297e837fca455d155 | 2022-03-28T08:43:05 | 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"
},
"sequenceId": "refseq:NC_000001.11",
"type": "SequenceLocation"
},
"referenceBases": "G",
"variantType": "SNP"
}
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 284e82aa022ef5eccc996d957e3af4fbf261c8c8 | 2022-02-24T11:37:28 | framework/json/responses/beaconMapResponse.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": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-unity-testing/main/framework/json/responses/sections/beaconInformationalResponseMeta.json",
"description": "Information about the response that could be relevant for the Beacon client in order to interpret the results."
},
"response": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-unity-testing/main/framework/json/configuration/beaconMapSchema.json",
"description": "Returning the Beacon Map."
}
},
"required": [
"meta",
"response"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 5468efe2aeea4398e89c1321ae060ceba835571e | 2023-06-04T13:51:19 | framework/json/responses/examples-fullDocuments/beaconInfo-MAX-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"info": {},
"meta": {
"apiVersion": "string",
"beaconId": "string",
"returnedSchemas": [
{
"entityType": "info",
"schema": "beacon-info-v2.0.0"
}
]
},
"response": {
"alternativeUrl": "https://example.org/wiki/Main_Page",
"apiVersion": "v0.3",
"createDateTime": "2012-07-19 or 2017-01-17T20:33:40Z",
"description": "string",
"environment": "dev",
"id": "org.ga4gh.beacon",
"info": {
"additionalInfoKey1": "additionalInfoValue1",
"additionalInfoKey2": [
"additionalInfoValue2",
"additionalInfoValue3"
]
},
"name": "string",
"organization": {
"address": "string",
"contactUrl": "string",
"description": "string",
"id": "string",
"info": {},
"logoUrl": "string",
"name": "string",
"welcomeUrl": "string"
},
"updateDateTime": "2012-07-19 or 2017-01-17T20:33:40Z",
"version": "v0.1",
"welcomeUrl": "https://example.org/wiki/Main_Page"
}
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 86d8c3bebb92dc892e2560022884e1ddea491821 | 2022-02-22T13:58:39 | framework/json/configuration/examples/beaconMap-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"endpointSets": {
"dataset": {
"endpoints": {
"exampleEntries": {
"returnedEntryType": "exampleEntry",
"url": "https://exampleBeacons.org/datasets/{id}/exampleEntries"
}
},
"entryType": "dataset",
"filteringTermsUrl": "https://exampleBeacons.org/datasets/{id}/filteringTerms",
"openAPIEndpointsDefinition": "./datasets/endpoints.json",
"rootUrl": "https://exampleBeacons.org/datasets",
"singleEntryUrl": "https://exampleBeacons.org/datasets/{id}"
},
"exampleEntry": {
"entryType": "exampleEntry",
"filteringTermsUrl": "https://exampleBeacons.org/exampleEntries/{id}/filteringTerms",
"openAPIEndpointsDefinition": "./exampleEntries/endpoints.json",
"rootUrl": "https://exampleBeacons.org/exampleEntries",
"singleEntryUrl": "https://exampleBeacons.org/exampleEntries/{id}"
}
}
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 8e09eabe19cfa57526eefd1765154ec2c985eede | 2022-10-11T11:03:58 | framework/json/responses/beaconBooleanResponse.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "Complete definition for a minimal response that provides *only* a `Boolean` exists true|false answer.",
"properties": {
"beaconHandovers": {
"$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": {
"$ref": "./sections/beaconBooleanResponseSection.json",
"description": "Boolean (true/false) response section."
}
},
"required": [
"meta",
"responseSummary"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 5468efe2aeea4398e89c1321ae060ceba835571e | 2023-06-04T13:51:19 | framework/json/responses/sections/beaconInfoResults.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"definitions": {
"BeaconOrganization": {
"description": "Organization owning the Beacon.",
"properties": {
"address": {
"description": "Address of the organization.",
"type": "string"
},
"contactUrl": {
"description": "URL with the contact for the Beacon operator/maintainer, e.g. link to a contact form (RFC 3986 format) or an email (RFC 2368 format).",
"type": "string"
},
"description": {
"description": "Description of the organization.",
"type": "string"
},
"id": {
"description": "Unique identifier of the organization.",
"type": "string"
},
"info": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/Info",
"description": "Additional unspecified metadata about the host Organization."
},
"logoUrl": {
"description": "URL to the logo (PNG/JPG/SVG format) of the organization (RFC 3986 format).",
"type": "string"
},
"name": {
"description": "Name of the organization.",
"type": "string"
},
"welcomeUrl": {
"description": "URL of the website of the organization (RFC 3986 format).",
"type": "string"
}
},
"required": [
"id",
"name"
],
"type": "object"
}
},
"description": "Metadata describing a Beacon instance.",
"properties": {
"alternativeUrl": {
"description": "Alternative URL to the API, e.g. a restricted version of this Beacon (RFC 3986 format).",
"examples": [
"https://example.org/beacon/authenticated"
],
"type": "string"
},
"apiVersion": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/ApiVersion"
},
"createDateTime": {
"description": "The date/time the Beacon was created (ISO 8601 format).",
"examples": [
"2014-07-19",
"2017-01-17 20:33:40"
],
"type": "string"
},
"description": {
"description": "Description of the Beacon.",
"type": "string"
},
"environment": {
"description": "Environment the service is running in. Use this to distinguish\nbetween production, development and testing/staging deployments.",
"enum": [
"prod",
"test",
"dev",
"staging"
],
"examples": [
"dev"
],
"type": "string"
},
"id": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/BeaconId"
},
"info": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/Info",
"description": "Additional unspecified metadata about the Beacon service."
},
"name": {
"description": "Name of the Beacon.",
"type": "string"
},
"organization": {
"$ref": "#/definitions/BeaconOrganization"
},
"updateDateTime": {
"description": "The time the Beacon was updated in (ISO 8601 format).",
"examples": [
"2014-07-19",
"2017-01-17 20:33:40"
],
"type": "string"
},
"version": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/ApiVersion",
"description": "TODO: This is a legacy use / duplication?"
},
"welcomeUrl": {
"description": "URL to the welcome page for this Beacon (RFC 3986 format).",
"example": "https://example.org/wiki/Main_Page",
"type": "string"
}
},
"required": [
"id",
"name",
"apiVersion",
"environment",
"organization"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 2a2b786e4a1845ea23d71dfe8125957b6f3d742f | 2022-06-20T13:19:32 | 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": "../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": {
"$ref": "./sections/beaconResultsets.json",
"description": "Response for queries that recovers any result."
},
"responseSummary": {
"$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 | 565e45856add68e73cab902635f1632bf9b40bb1 | 2022-12-22T09:27:04 | 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"
},
"beaconId": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/BeaconId"
},
"receivedRequestSummary": {
"$ref": "./beaconReceivedRequestSummary.json"
},
"returnedGranularity": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/Granularity",
"description": "Granularity of the Beacon response which may differ from the requested one. For details see the prototype definition."
},
"returnedSchemas": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/ListOfSchemas",
"description": "The `returnedSchemas` parameter indicates that the request has been interpreted for the indicated entity. This helps to disambiguate between negative responses due to e.g. no hit on a well understood request and failures to interpret or answer the request due to a missing entity. "
},
"testMode": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/TestMode"
}
},
"required": [
"beaconId",
"apiVersion",
"returnedSchemas",
"returnedGranularity",
"receivedRequestSummary"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | f3f93ef9f94f0164a185d36dd45045fc1a179c14 | 2022-12-21T19:45:33 | framework/json/responses/sections/beaconInfoResults.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"definitions": {
"BeaconOrganization": {
"description": "Organization owning the Beacon.",
"properties": {
"address": {
"description": "Address of the organization.",
"type": "string"
},
"contactUrl": {
"description": "URL with the contact for the Beacon operator/maintainer, e.g. link to a contact form (RFC 3986 format) or an email (RFC 2368 format).",
"type": "string"
},
"description": {
"description": "Description of the organization.",
"type": "string"
},
"id": {
"description": "Unique identifier of the organization.",
"type": "string"
},
"info": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/Info",
"description": "Additional unspecified metadata about the host Organization."
},
"logoUrl": {
"description": "URL to the logo (PNG/JPG/SVG format) of the organization (RFC 3986 format).",
"type": "string"
},
"name": {
"description": "Name of the organization.",
"type": "string"
},
"welcomeUrl": {
"description": "URL of the website of the organization (RFC 3986 format).",
"type": "string"
}
},
"required": [
"id",
"name"
],
"type": "object"
}
},
"description": "Metadata describing a Beacon instance.",
"properties": {
"alternativeUrl": {
"description": "Alternative URL to the API, e.g. a restricted version of this Beacon (RFC 3986 format).",
"examples": [
"http://example.org/beacon/authenticated"
],
"type": "string"
},
"apiVersion": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/ApiVersion"
},
"createDateTime": {
"description": "The date/time the Beacon was created (ISO 8601 format).",
"examples": [
"2014-07-19",
"2017-01-17 20:33:40"
],
"type": "string"
},
"description": {
"description": "Description of the Beacon.",
"type": "string"
},
"environment": {
"description": "Environment the service is running in. Use this to distinguish\nbetween production, development and testing/staging deployments.",
"enum": [
"prod",
"test",
"dev",
"staging"
],
"examples": [
"dev"
],
"type": "string"
},
"id": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/BeaconId"
},
"info": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/Info",
"description": "Additional unspecified metadata about the Beacon service."
},
"name": {
"description": "Name of the Beacon.",
"type": "string"
},
"organization": {
"$ref": "#/definitions/BeaconOrganization"
},
"updateDateTime": {
"description": "The time the Beacon was updated in (ISO 8601 format).",
"examples": [
"2014-07-19",
"2017-01-17 20:33:40"
],
"type": "string"
},
"version": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/ApiVersion",
"description": "TODO: This is a legacy use / duplication?"
},
"welcomeUrl": {
"description": "URL to the welcome page for this Beacon (RFC 3986 format).",
"example": "http://example.org/wiki/Main_Page",
"type": "string"
}
},
"required": [
"id",
"name",
"apiVersion",
"environment",
"organization"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 3e6093cf1b20ac74bc021c315511094f930be1ef | 2022-02-22T11:21:39 | framework/json/responses/sections/beaconSummaryResponseSection.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "Beacon results summary section.",
"properties": {
"exists": {
"$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": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/NumTotalResults",
"description": "Total number of results."
}
},
"required": [
"exists"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 89f9aacffcb00b3395ffa9d908cf38c7bb598b5e | 2022-03-23T07:55:42 | models/json/beacon-v2-default-model/common/procedure.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "Class describing a clinical procedure or intervention. Provenance: GA4GH Phenopackets v2 `Procedure`",
"properties": {
"ageAtProcedure": {
"$ref": "./timeElement.json",
"description": "Compares to Phenopackets v2 `Procedure.performed`"
},
"bodySite": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json",
"description": "Specific body site where the procedure was performed. Recommended valuee from Uber-anatomy ontology (UBERON)",
"examples": [
{
"id": "UBERON:0003403",
"label": "Skin of forearm"
},
{
"id": "UBERON:0003214",
"label": "mammary gland alveolus"
}
]
},
"dateOfProcedure": {
"description": "Date of procedure, in ISO8601 format",
"example": "2010-07-10",
"format": "date",
"type": "string"
},
"procedureCode": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json",
"description": "Clinical procedure performed with recommended values from Medical Action Ontology (MAXO) 'Medical action' term tree (MAXO:0000001). Compares to Phenopackets v2 `Procedure.code`",
"examples": [
{
"id": "MAXO:0001175",
"label": "liver transplantation"
},
{
"id": "MAXO:0000136",
"label": "high-resolution microendoscopy"
},
{
"id": "OBI:0002654",
"label": "needle biopsy"
}
]
}
},
"required": [
"procedureCode"
],
"title": "Procedure",
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 030747a0ef492bd79dc53d3eaf9f6c16ceae236a | 2022-02-22T13:50:28 | framework/json/responses/examples-sections/beaconResultsets-MIN-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"resultSets": []
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 89ed443fecde703f259d5ec169ceeede37db72f9 | 2022-03-09T07:58:30 | 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": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-unity-testing/main/framework/json/common/ontologyTerm.json",
"description": "Disease identifier. Value from disease ontologies such as HPO, OMIM, Orphanet, MONDO, e.g. lactose intolerance (HP:0004789, ICD10CM:E73). Provenance: GA4GH Phenopackets v2 `Disease.term`",
"examples": [
{
"id": "HP:0004789",
"label": "lactose intolerance"
},
{
"id": "ICD10CM:E73",
"label": "lactose intolerance"
},
{
"id": "OMIM:164400",
"label": "Spinocerebellar ataxia 1"
}
]
},
"familyHistory": {
"description": "Boolean indicating determined or self-reported presence of family history of the disease.",
"example": true,
"type": "boolean"
},
"notes": {
"description": "Unstructured text to describe additional properties of this disease instance.",
"example": "Some free text",
"type": "string"
},
"severityLevel": {
"$ref": "./commonDefinitions.json#/definitions/SeverityLevel"
},
"stage": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-unity-testing/main/framework/json/common/ontologyTerm.json",
"description": "Ontology term from Ontology for General Medical Science (OGMS), e.g. acute onset (OGMS:0000119). Provenance: GA4GH Phenopackets v2 `Disease.disease_stage`",
"examples": [
{
"id": "OGMS:0000119",
"label": "acute onset"
},
{
"id": "OGMS:0000117",
"label": "asymptomatic"
},
{
"id": "OGMS:0000106",
"label": "remission"
}
]
}
},
"required": [
"diseaseCode"
],
"title": "Disease",
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 3e6093cf1b20ac74bc021c315511094f930be1ef | 2022-02-22T11:21:39 | framework/json/requests/beaconRequestMeta.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "Meta section of the Beacon request. It includes request context details relevant for the Beacon server when processing the request.",
"properties": {
"$schema": {
"$ref": "../common/beaconCommonComponents.json#/definitions/$schema"
},
"apiVersion": {
"$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."
},
"requestedSchemas": {
"$ref": "../common/beaconCommonComponents.json#/definitions/ListOfSchemas",
"description": "Set of schemas to be used in the response."
}
},
"required": [
"apiVersion"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 3e6093cf1b20ac74bc021c315511094f930be1ef | 2022-02-22T11:21:39 | framework/json/common/elementWithDescription.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"allOf": [
{
"$ref": "./basicElement.json"
},
{
"properties": {
"description": {
"description": "A textual description for the element.",
"type": "string"
}
},
"type": "object"
}
],
"description": "Definition of the basic element extended with a description.",
"title": "Basic Element including a description",
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 89ed443fecde703f259d5ec169ceeede37db72f9 | 2022-03-09T07:58:30 | models/json/beacon-v2-default-model/common/complexValue.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"definitions": {
"TypedQuantity": {
"properties": {
"quantity": {
"$ref": "./quantity.json",
"description": "Quantity denoting the outcome of the measurement",
"example": {
"quentity": {
"unit": {
"id": "NCIT:C49670",
"label": "Millimeter of Mercury"
}
}
}
},
"quantityType": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-unity-testing/main/framework/json/common/ontologyTerm.json",
"description": "OntologyClass to describe the type of the measurement. Renamed compared to GA4GH Phenopackets v2 `ComplexValue.TypedQuantity.type`",
"example": {
"id": "NCIT:C25298",
"label": "Systolic Blood Pressure"
}
}
},
"required": [
"quantityType",
"quantity"
]
}
},
"description": "Definition of a complex value class. Provenance: GA4GH Phenopackets v2 `TypedQuantity`",
"properties": {
"typedQuantities": {
"description": "List of quantities required to fully describe the complex value",
"items": {
"$ref": "#/definitions/TypedQuantity"
},
"type": "array"
}
},
"title": "Complex Value",
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 07f7c579309f8fbed64324f396199a4aa31c16c4 | 2022-03-30T12:20:02 | models/json/beacon-v2-default-model/biosamples/examples/biosample-MID-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"biosampleStatus": {
"id": "EFO:0009655",
"label": "abnormal sample"
},
"collectionDate": "2020-09-11",
"collectionMoment": "P32Y6M1D",
"id": "sample-example-0001",
"obtentionProcedure": {
"procedureCode": {
"id": "OBI:0002654",
"label": "needle biopsy"
}
},
"sampleOriginType": {
"id": "UBERON:0000992",
"label": "ovary"
}
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 030747a0ef492bd79dc53d3eaf9f6c16ceae236a | 2022-02-22T13:50:28 | framework/json/responses/sections/beaconResultsets.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"definitions": {
"ResultsetInstance": {
"additionalProperties": true,
"properties": {
"exists": {
"type": "boolean"
},
"id": {
"description": "id of the resultset",
"example": "datasetA",
"type": "string"
},
"info": {
"description": "Additional details that could be of interest about the Resultset. Provided to clearly enclose any attribute that is not part of the Beacon specification.",
"type": "object"
},
"results": {
"items": {
"type": "object"
},
"minItems": 0,
"type": "array"
},
"resultsCount": {
"description": "Number of results in this Resulset.",
"type": "integer"
},
"resultsHandovers": {
"$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 | 5468efe2aeea4398e89c1321ae060ceba835571e | 2023-06-04T13:51:19 | models/json/beacon-v2-default-model/datasets/examples/dataset-Max-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"createDateTime": "2017-01-17T20:33:40Z",
"dataUseConditions": {
"duoDataUse": [
{
"id": "DUO:0000007",
"label": "disease specific research",
"modifiers": [
{
"id": "EFO:0001645",
"label": "coronary artery disease"
}
],
"version": "17-07-2016"
}
]
},
"description": "This dataset provides examples of the actual data in this Beacon instance.",
"externalUrl": "https://example.org/wiki/Main_Page",
"id": "ds01010101",
"name": "Dataset with synthetic data",
"updateDateTime": "2017-01-17T20:33:40Z",
"version": "v1.1"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | af5cda939ff4e14fef57becbd05ccc3da6adc8a5 | 2022-06-20T09:22:16 | models/json/beacon-v2-default-model/genomicVariations/requestParameters.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$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 (0-based, inclusive). * `start` only:\n - for single positions, e.g. the start of a specified sequence\n alteration where the size is given through the specified `alternateBases`\n - typical use are queries for SNV and small InDels\n - the use of `start` without an `end` parameter requires the use of\n `alternateBases`\n* `start` and `end`:\n - for searching any variant falling fully or partially within the range\n 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 genomic\n range are accepted; for specific overlap requirements the 4-parameter\n \"Bracket Queries\" should be employed\n* 2 values in both `start` and `end` for constructing a \"Bracket Query\":\n - can be used to match any contiguous genomic interval, e.g. for querying\n imprecise positions\n - identifies all structural variants starting between `start[0]` and `start[1]`,\n and ending between `end[0]` <-> `end[1]`\n - single or double sided precise matches can be achieved by setting\n `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 | 89f9aacffcb00b3395ffa9d908cf38c7bb598b5e | 2022-03-23T07:55:42 | models/json/beacon-v2-default-model/common/pedigree.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"definitions": {
"pedigreeMember": {
"examples": [
{
"membersInProband": [
{
"affected": true,
"memberId": "Ind0012122",
"role": {
"id": "NCIT:C64435",
"label": "Proband"
}
},
{
"affected": false,
"memberId": "Pedigree1001-m2",
"role": {
"id": "NCIT:C96580",
"label": "Biological Mother"
}
},
{
"affected": true,
"memberId": "Pedigree1001-m3",
"role": {
"id": "NCIT:C96572",
"label": "Biological Father"
}
}
]
},
{
"membersInMother": [
{
"affected": false,
"memberId": "Ind0028989",
"role": {
"id": "NCIT:C96580",
"label": "Biological Mother"
}
},
{
"affected": true,
"memberId": "Ind0012122",
"role": {
"id": "NCIT:C64435",
"label": "Proband"
}
}
]
}
],
"properties": {
"affected": {
"description": "Is the individual affected by the disease in the pedigree?",
"type": "boolean"
},
"memberId": {
"description": "Identifier of the individual. The individual could be part of the same Beacon datasets or not, in which case the information here is meant to complete the pedigree. If the individual is also in the dataset use that Individual ID. If it is not the in the dataset, use a non-collading ID, e.g. concatenating the Pedigree ID with a local ID, similarly to the example 'Pedigree1001-m1'.",
"examples": [
"Pedigree1001-m1",
"Ind0012122"
],
"type": "string"
},
"role": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json",
"description": "Pedigree role, defined as relationship to proband. Value from Family Member term (NCIT:C41256), e.g. \"proband\" (NCIT:C64435),\"identical twin\" (NCIT:C73429), \"mother\" (NCIT:C25189).",
"examples": [
{
"id": "NCIT:C64435",
"label": "Proband"
},
{
"id": "NCIT:C96580",
"label": "Biological Mother"
},
{
"id": "NCIT:C96572",
"label": "Biological Father"
},
{
"id": "NCIT:C165848",
"label": "Identical Twin Brother"
}
]
}
},
"required": [
"memberId",
"role",
"affected"
],
"type": "object"
}
},
"description": "Pedigree studies in which the individual is part of.",
"properties": {
"disease": {
"$ref": "../common/disease.json"
},
"id": {
"description": "Pedigree identifier.",
"example": "Pedigree1001",
"type": "string"
},
"members": {
"description": "List of members of the pedigree. If the current pedigree definition is attached to the proband, it contains the whole list of pedigree members, including the proband. If the definition is attached to an individual different than the proband, it only contains two entries: one that describes that member, e.g. the proband mother or father, and one that points to the proband.",
"items": {
"$ref": "#/definitions/pedigreeMember"
},
"minItems": 1,
"type": "array"
},
"numSubjects": {
"description": "Total number of subjects in pedigree.",
"example": 10,
"type": "integer"
}
},
"required": [
"id",
"disease",
"members"
],
"title": "Pedigree",
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 7c301c464130f518093f885e8c323786e340abf3 | 2023-02-17T08:29:10 | models/json/beacon-v2-default-model/genomicVariations/requestParameters.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$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: * (0-based, exclusive) - see `start` * 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": "* A gene identifier * It is strongly suggested to use a symbol following\n 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 (0-based, inclusive). * `start` only:\n - for single positions, e.g. the start of a specified sequence\n alteration where the size is given through the specified `alternateBases`\n - typical use are queries for SNV and small InDels\n - the use of `start` without an `end` parameter requires the use of\n `alternateBases`\n* `start` and `end`:\n - for searching any variant falling fully or partially within the range\n 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 genomic\n range are accepted; for specific overlap requirements the 4-parameter\n \"Bracket Queries\" should be employed\n* 2 values in both `start` and `end` for constructing a \"Bracket Query\":\n - can be used to match any contiguous genomic interval, e.g. for querying\n imprecise positions\n - identifies all structural variants starting between `start[0]` and `start[1]`,\n and ending between `end[0]` <-> `end[1]`\n - single or double sided precise matches can be achieved by setting\n `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\n commonly available for structural variants such as copy number variations,\n it is recommended that length based queries should also be supported for\n variants with indicated referenceBases and alternateBases, to enable\n 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\n commonly available for structural variants such as copy number variations,\n it is recommended that length based queries should also be supported for\n variants with indicated referenceBases and alternateBases, to enable\n length-specific wildcard queries.",
"format": "int64",
"minimum": 0,
"type": "integer"
},
"variantType": {
"description": "The `variantType` is used to query variants which are not defined through a sequence of one or more bases using the `alternateBases` parameter. Examples here are e.g. structural variants: * DUP\n - increased allelic count of material from the genomic region between\n `start` and `end` positions\n - no assumption about the placement of the additional sequences is being\n made (i.e. no _in situ_ requirement as tandem duplications)\n* DEL: deletion of sequence following `start` The Beacon model is not prescriptive with regard to the values allowed for `variantType` with use of extended types (such as from `EFO:0030063`) being permitted. However, a support for the basic CNV types above - where represented in the data - is recommended.",
"examples": [
"EFO:0030070",
"DUP",
"DEL",
"EFO:0030069"
],
"type": "string"
}
},
"type": "object"
}
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 89ed443fecde703f259d5ec169ceeede37db72f9 | 2022-03-09T07:58:30 | models/json/beacon-v2-default-model/biosamples/examples/biosample-MID-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"biosampleStatus": {
"id": "EFO:0009655",
"label": "abnormal sample"
},
"collectionDate": "2020-09-11",
"collectionMoment": "P32Y6M1D",
"id": "sample-example-0001",
"obtentionProcedure": {
"code": {
"id": "OBI:0002654",
"label": "needle biopsy"
}
},
"sampleOriginType": {
"id": "UBERON:0000992",
"label": "ovary"
}
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 86d8c3bebb92dc892e2560022884e1ddea491821 | 2022-02-22T13:58:39 | framework/json/responses/sections/beaconSummaryResponseSection.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "Beacon results summary section.",
"properties": {
"exists": {
"$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": {
"$ref": "../../common/beaconCommonComponents.json#/definitions/NumTotalResults",
"description": "Total number of results."
}
},
"required": [
"exists"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 86d8c3bebb92dc892e2560022884e1ddea491821 | 2022-02-22T13:58:39 | framework/json/requests/beaconRequestBody.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$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 that is relevant to build 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": {
"$ref": "../common/beaconCommonComponents.json#/definitions/Pagination",
"description": "Pagination to apply on the results."
},
"requestParameters": {
"$ref": "./requestParameters.json",
"description": "TBD"
},
"requestedGranularity": {
"$ref": "../common/beaconCommonComponents.json#/definitions/Granularity",
"description": "Requested granularity. Targeted Beacon could respond or not with the requested granularity. E.g. record level granularity could be requested, but the Beacon could respond only with boolean or count results."
},
"testMode": {
"$ref": "../common/beaconCommonComponents.json#/definitions/TestMode",
"description": "Used for indicating that a request or response is done in a test context. Purposed for compliance testing."
}
},
"type": "object"
}
},
"required": [
"meta"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 86d8c3bebb92dc892e2560022884e1ddea491821 | 2022-02-22T13:58:39 | framework/json/responses/examples-fullDocuments/beaconCountResponse-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"beaconHandovers": [
{
"handoverType": {
"id": "EFO:0004157",
"label": "BAM format"
},
"note": "This handover link provides access to a summarized VCF.",
"url": "https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0"
},
{
"handoverType": {
"id": "EFO:0004157",
"label": "BAM format"
},
"note": "This handover link provides access to a summarized VCF.",
"url": "https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0"
}
],
"info": {
"someInterestingStuff": "this is the interesting stuff"
},
"meta": {
"apiVersion": "v2.0",
"beaconId": "org.example.beacon.v2",
"receivedRequestSummary": {
"apiVersion": "2.0",
"pagination": {
"limit": 10,
"skip": 0
},
"requestedSchemas": [
{
"entityType": "EntryTypeB",
"schema": "entry-typeB-schema-v1.0"
}
]
},
"returnedSchemas": [
{
"entityType": "EntryTypeB",
"schema": "entry-typeB-schema-v1.0"
}
]
},
"responseSummary": {
"exists": true,
"numTotalResults": 25355
}
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 030747a0ef492bd79dc53d3eaf9f6c16ceae236a | 2022-02-22T13:50:28 | framework/json/requests/examples-fullDocuments/beaconRequestBody-MIN-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"meta": {
"apiVersion": "2.0"
}
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 69ac9bfcbbefaa9700ba20f411ccdbc8237a157b | 2022-08-22T09:32:44 | 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 of 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": {
"$ref": "../common/beaconCommonComponents.json#/definitions/TestMode",
"description": "Used for indicating that a request or response is done in a test context. Necessary for compliance testing, e.g. to have an assessment of responses w/o the need to use specific query values generating a positive response from a tested Beacon. Responses to _testMode_ requests should use synthetic or other privacy preserving data."
}
},
"type": "object"
}
},
"required": [
"meta"
],
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 1c03b708fdfd3e822886f51f0bb20f658030f76c | 2022-03-28T12:54:26 | models/json/beacon-v2-default-model/cohorts/examples/cohorts-MAX-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$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",
"collectionEvents": [
{
"eventDataTypes": {
"availability": true,
"distribution": {
"dataTypes": {
"blood collected from fasting subject": 51,
"survey data": 98
}
}
},
"eventDate": "2019-04-23",
"eventEthnicities": {
"availability": true,
"availabilityCount": 101,
"distribution": {
"ethnicities": {
"African": 3,
"European": 90,
"Latin American": 8
}
}
},
"eventGenders": {
"availability": true,
"availabilityCount": 101,
"distribution": {
"genders": {
"female": 51,
"male": 50
}
}
},
"eventNum": 1,
"eventSize": 101
}
],
"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 | 89ed443fecde703f259d5ec169ceeede37db72f9 | 2022-03-09T07:58:30 | models/json/beacon-v2-default-model/common/exposure.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"description": "Exposures (lifestyle, behavioural exposures) occurred to individual,defined by exposure ID, date and age of onset, dose, and duration.",
"properties": {
"ageAtExposure": {
"$ref": "../common/age.json"
},
"date": {
"description": "Date of the exposure in ISO8601 format.",
"format": "date",
"type": "string"
},
"duration": {
"description": "Exposure duration in ISO8601 format",
"example": "P32Y6M1D",
"type": "string"
},
"exposureCode": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-unity-testing/main/framework/json/common/ontologyTerm.json",
"description": "Exposure ID. Value from Environment Exposure Ontology.",
"examples": [
{
"id": "CHEBI:46661",
"label": "asbestos"
},
{
"id": "ENVO:21001217",
"label": "X-ray radiation"
}
]
},
"unit": {
"$ref": "../common/commonDefinitions.json#/definitions/Unit",
"description": "Unit of the exposure. Recommended from NCIT Unit of Category ontology term (NCIT:C42568) descendants."
},
"value": {
"description": "Quantification of the exposure.",
"type": "number"
}
},
"required": [
"exposureCode",
"ageAtExposure",
"units",
"duration"
],
"title": "Procedure",
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 89ed443fecde703f259d5ec169ceeede37db72f9 | 2022-03-09T07:58:30 | 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": {
"$ref": "./age.json",
"description": "Represents age as an ISO8601 duration (e.g., P18Y)."
}
},
"title": "AgeRange",
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 9eaada7ca0410f4127d0c324880033e60024d128 | 2022-03-13T12:14:16 | models/json/beacon-v2-default-model/runs/examples/runs-MAX-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"biosampleId": "008dafdd-a3d1-4801-8c0a-8714e2b58e48",
"id": "SRR10903401",
"individualId": "TCGA-AO-A0JJ",
"libraryLayout": "PAIRED",
"librarySelection": "RANDOM",
"librarySource": {
"id": "GENEPIO:0001966",
"label": "genomic source"
},
"libraryStrategy": "WGS",
"platform": "Illumina",
"platformModel": {
"id": "OBI:0002048",
"label": "Illumina HiSeq 3000"
},
"runDate": "2021-10-18"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 030747a0ef492bd79dc53d3eaf9f6c16ceae236a | 2022-02-22T13:50:28 | framework/json/common/ontologyTerm.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"definitions": {
"CURIE": {
"description": "A CURIE identifier for an ontology term.",
"examples": [
"ga4gh:GA.01234abcde",
"DUO:0000004",
"orcid:0000-0003-3463-0775",
"PMID:15254584"
],
"pattern": "^\\w[^:]+:.+$",
"type": "string"
}
},
"description": "Definition of an ontology term.",
"properties": {
"id": {
"$ref": "#/definitions/CURIE"
},
"label": {
"description": "The text that describes the term. By default it could be the preferred text of the term, but is it acceptable to customize it for a clearer description and understanding of the term in an specific context.",
"type": "string"
}
},
"required": [
"id"
],
"title": "Ontology Term",
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 0d0aee6316a240037f5dd952bf70eb5f26c65a61 | 2022-03-29T15:12:03 | models/json/beacon-v2-default-model/common/exposure.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"description": "Exposures (lifestyle, behavioural exposures) occurred to individual,defined by exposure ID, date and age of onset, dose, and duration.",
"properties": {
"ageAtExposure": {
"$ref": "../common/age.json"
},
"date": {
"description": "Date of the exposure in ISO8601 format.",
"format": "date",
"type": "string"
},
"duration": {
"description": "Exposure duration in ISO8601 format",
"example": "P32Y6M1D",
"type": "string"
},
"exposureCode": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json",
"description": "Exposure ID. Value from Environment Exposure Ontology.",
"examples": [
{
"id": "CHEBI:46661",
"label": "asbestos"
},
{
"id": "ENVO:21001217",
"label": "X-ray radiation"
}
]
},
"unit": {
"$ref": "../common/commonDefinitions.json#/definitions/Unit",
"description": "Unit of the exposure. Recommended from NCIT Unit of Category ontology term (NCIT:C42568) descendants."
},
"value": {
"description": "Quantification of the exposure.",
"type": "number"
}
},
"required": [
"exposureCode",
"ageAtExposure",
"unit",
"duration"
],
"title": "Exposure",
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 86d8c3bebb92dc892e2560022884e1ddea491821 | 2022-02-22T13:58:39 | framework/json/requests/examples-sections/beaconRequestMeta-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"apiVersion": "2.0",
"requestedSchemas": [
{
"entityType": "EntryTypeA",
"schema": "entry-typeA-schema-v0.1"
}
]
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 3e6093cf1b20ac74bc021c315511094f930be1ef | 2022-02-22T11:21:39 | framework/json/requests/examples-sections/requestParameters-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"exampleEntry": {
"description": "All the required fields to query any kind of variant (e.g. SNP, DUP,\netc.).",
"properties": {
"id": {
"description": "Id of the entry to display.",
"type": "string"
}
},
"type": "object"
}
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 2a2b786e4a1845ea23d71dfe8125957b6f3d742f | 2022-06-20T13:19:32 | framework/json/responses/beaconEntryTypesResponse.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"description": "Response including a list of Entry types definitions.",
"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/entryTypesSchema.json",
"description": "Returning the Beacon Entry Types."
}
},
"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-MAX-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"IncludeResultsetResponses": "HIT",
"apiVersion": "v2.0",
"filters": [
"BTO:0000199",
"PATO:0000383"
],
"pagination": {
"limit": 10,
"skip": 1
},
"requestParameters": {
"individual": {
"parameters": [
{
"id": "123"
}
]
}
},
"requestedGranularity": "count",
"requestedSchemas": [
{
"entityType": "Individual",
"schema": "ga4gh-phenopacket-individual-v0.1"
}
],
"testMode": false
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 030747a0ef492bd79dc53d3eaf9f6c16ceae236a | 2022-02-22T13:50:28 | framework/json/common/examples/referenceToAnSchema-MIN-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"id": "RTAEex1",
"name": "Reference to schema one with all its properties.",
"referenceToSchemaDefinition": "https://example-schemas.org/an-schema-address.json"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 7c301c464130f518093f885e8c323786e340abf3 | 2023-02-17T08:29:10 | models/json/beacon-v2-default-model/genomicVariations/requestParametersComponents.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"definitions": {
"AlternateBases": {
"description": "Alternate bases for this variant (starting from `start`). * Accepted values: `[ACGTN]*` * The current specification supports allelic variants, **not** genotype queries\n (i.e. multiple co-occurring alleles).\n* N is a wildcard, that denotes the position of any base,\n and can be used as a standalone base of any type or within a partially known\n sequence. As example, a query of `ANNT` the Ns can take take any form of [ACGT]\n and will match `ANNT`, `ACNT`, `ACCT`, `ACGT` ... and so forth.\n* an *empty value* is used in the case of deletions with the maximally trimmed,\n deleted sequence being indicated in `ReferenceBases`\n* Categorical variant queries, e.g. such *not* being represented through\n sequence & position, make use of the `variantType` parameter.",
"pattern": "^([ACGTUNRYSWKMBDHV\\-\\.]*)$",
"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\\-\\.]*)$",
"type": "string"
}
},
"description": "Component definitions used in `requestParameters`."
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 3e6093cf1b20ac74bc021c315511094f930be1ef | 2022-02-22T11:21:39 | framework/json/responses/examples-fullDocuments/beaconFilteringTermsResponse-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"info": {},
"meta": {
"apiVersion": "string",
"beaconId": "string",
"returnedSchemas": [
{
"map": "beacon-map-v2.0.0"
}
]
},
"response": {
"filteringTerms": [
{
"id": "PATO:0000011",
"label": "age",
"type": "numeric"
},
{
"id": "HP:0008773",
"label": "Aplasia/Hypoplasia of the middle ear",
"type": "Human Phenotype Ontology"
},
{
"id": "ownsIPhone",
"label": "Individuals associated with this term owns an IPhone",
"type": "custom"
}
],
"resources": [
{
"id": "hp",
"iriPrefix": "http://purl.obolibrary.org/obo/HP_",
"name": "Human Phenotype Ontology",
"namespacePrefix": "HP",
"url": "http://purl.obolibrary.org/obo/hp.owl",
"version": "27-03-2020"
}
]
}
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 89ed443fecde703f259d5ec169ceeede37db72f9 | 2022-03-09T07:58:30 | models/json/beacon-v2-default-model/analyses/filteringTerms.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"filteringTerms": []
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 284e82aa022ef5eccc996d957e3af4fbf261c8c8 | 2022-02-24T11:37:28 | framework/json/responses/examples-fullDocuments/beaconConfigurationResponse-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$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": {
"$schema": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-unity-testing/main/framework/json/configuration/beaconConfigurationSchema.json",
"entryTypes": {
"dataset": {
"aCollectionOf": [
{
"id": "exampleEntry",
"name": "Example entries"
}
],
"additionallySupportedSchemas": [],
"defaultSchema": {
"id": "datasetDefaultSchema",
"name": "Default schema for datasets",
"referenceToSchemaDefinition": "./datasets/defaultSchema.json",
"schemaVersion": "v.2"
},
"description": "A Dataset is a collection of records, like rows in a database or cards in a cardholder.",
"endpoint": "/datasets",
"filteringTermsReference": "./datasets/filteringTerms.json",
"id": "dataset",
"name": "Dataset",
"ontologyTermForThisType": {
"id": "NCIT:C47824",
"label": "Data set"
},
"partOfSpecification": "Beacon v2.0"
},
"exampleEntry": {
"additionallySupportedSchemas": [],
"defaultSchema": {
"id": "ExampleEntryTypeDefaultschema",
"name": "Default schema for an example entries",
"referenceToSchemaDefinition": "./exampleEntry/defaultSchema.json",
"schemaVersion": "v.2"
},
"description": "A generic entry type to allow testing and playing with the specification.",
"endpoint": "./exampleEntries",
"filteringTermsReference": "./exampleEntry/filteringTerms.json",
"id": "exampleEntry",
"name": "Example Entry",
"ontologyTermForThisType": {
"id": "NCIT:C20181",
"label": "Conceptual Entity"
},
"partOfSpecification": "Beacon v2.0"
}
},
"maturityAttributes": {
"productionStatus": "DEV"
},
"securityAttributes": {
"defaultGranularity": "boolean",
"securityLevels": [
"PUBLIC",
"REGISTERED",
"CONTROLLED"
]
}
}
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | bf2d78821c80404be777c9f0df35f79e8424bbd6 | 2022-03-24T08:35:39 | models/json/beacon-v2-default-model/individuals/examples/individual-MID-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$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,
"severity": {
"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 | 030747a0ef492bd79dc53d3eaf9f6c16ceae236a | 2022-02-22T13:50:28 | framework/json/configuration/examples/beaconMap-MIN-example.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"endpointSets": {
"datasets": {
"entryType": "dataset",
"rootUrl": "https://exampleBeacons.org/datasets"
}
}
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 3e6093cf1b20ac74bc021c315511094f930be1ef | 2022-02-22T11:21:39 | framework/json/configuration/beaconMapSchema.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"definitions": {
"Endpoint": {
"properties": {
"endpoints": {
"additionalProperties": {
"$ref": "#/definitions/RelatedEndpoint"
},
"description": "Optional. A list describing additional endpoints implemented by this Beacon instance for that entry type. Additional details on the endpoint parameters, supported HTTP verbs, etc. could be obtained by parsing the OpenAPI definition referenced in the `openAPIEndpointsDefinition` attribute.",
"minProperties": 0,
"type": "object"
},
"entryType": {
"description": "",
"type": "string"
},
"filteringTermsUrl": {
"description": "Optional. Returns the list of filtering terms that could be applied to this entry type. It is added here for convenience of the Beacon clients, so they don't need to parse the OpenAPI endpoints definition to get that endpoint. Also, in very simple Beacons, that endpoint could be the one of the few implemented, together with \u00b4rootUrl` and \u00b4singleEntryUrl`, in which case the whole map of endpoints is found in the current Map.",
"format": "uri",
"type": "string"
},
"openAPIEndpointsDefinition": {
"description": "Reference to the file that includes the OpenAPI definition of the endpoints implemented in this Beacon instance. The referenced file MUST BE a valid OpenAPI definition file, as it is expected that the Beacon clients (e.g. a Beacon Network) should be able to parse it to discover additional details on the supported verbs, parameters, etc.",
"type": "string"
},
"rootUrl": {
"description": "The base url for this entry type. Returns a list of entries. It is added here for convenience of the Beacon clients, so they don't need to parse the OpenAPI endpoints definition to get that base endpoint. Also, in very simple Beacons, that endpoint could be the only one implemented, together with \u00b4singleEntryUrl`, in which case the whole map of endpoints is found in the current Map.",
"format": "uri",
"type": "string"
},
"singleEntryUrl": {
"description": "Optional, but recommended. Returns only one instance of this entry, identified by an `id`. It is added here for convenience of the Beacon clients, so they don't need to parse the OpenAPI endpoints definition to get that base endpoint. Also, in very simple Beacons, that endpoint could be the only one implemented, together with \u00b4rootUrl`, in which case the whole map of endpoints is found in the current Map.",
"format": "uri",
"type": "string"
}
},
"required": [
"entryType",
"rootUrl"
],
"type": "object"
},
"RelatedEndpoint": {
"properties": {
"returnedEntryType": {
"description": "Which entry type is returned by querying this endpoint. It MUST match one of the entry types defined in the Beacon configuration file (`beaconConfiguration.json`).",
"type": "string"
},
"url": {
"description": "Endpoint URL",
"format": "uri",
"type": "string"
}
},
"required": [
"url",
"returnedEntryType"
],
"type": "object"
}
},
"description": "Map of a Beacon, its entry types and endpoints. It is conceptually similar to a website sitemap.",
"properties": {
"$schema": {
"$ref": "../common/beaconCommonComponents.json#/definitions/$schema"
},
"endpointSets": {
"additionalProperties": {
"$ref": "#/definitions/Endpoint"
},
"description": "List of enpoints included in this Beacon instance. This is list is meant to inform Beacon clients, e.g. a Beacon Network, about the available endpoints, it is not used to generate any automatic list, but could be used for Beacon validation purposes.",
"minProperties": 1,
"type": "object"
}
},
"required": [
"$schema",
"endpointSets"
],
"title": "Beacon Map",
"type": "object"
} | CC0-1.0 | en |
ga4gh-beacon/beacon-v2 | 3e6093cf1b20ac74bc021c315511094f930be1ef | 2022-02-22T11:21:39 | 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-unity/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 | 89ed443fecde703f259d5ec169ceeede37db72f9 | 2022-03-09T07:58:30 | models/json/beacon-v2-default-model/common/evidence.json | 21 | 2024-05-27T06:03:09.146153Z | {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"description": "Definition of an evidence class. Provenance: GA4GH Phenopackets v2 `Evidence`",
"properties": {
"evidenceCode": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-unity-testing/main/framework/json/common/ontologyTerm.json",
"description": "An ontology class that represents the evidence type",
"example": {
"id": "ECO:0006017",
"label": "author statement from published clinical study used in manual assertion"
}
},
"reference": {
"$ref": "./externalReference.json",
"description": "Representation of the source of the evidence",
"example": {
"id": "PMID:30962759",
"label": "Recurrent Erythema Nodosum in a Child with a SHOC2 Gene Mutation"
}
}
},
"required": [
"evidenceCode"
],
"title": "Evidence",
"type": "object"
} | CC0-1.0 | en |
Subsets and Splits