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default_interactor_schema.yaml
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default_interactor_schema.yaml
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openapi: 3.0.2
servers: []
info:
version: "draft.3"
title: GA4GH Beacon Interactor Default Schema
description: |
Schema for interactor to be used as default by the Beacon.
This object contains info related to the subject from where the variants are found in a study.
It includes taxon id and any other relevant information about it, including maybe links or id
of genome assemblies and ref seqs associated to this species that are available in the Beacon
and that are used for variant identification (location)
contact:
email: [email protected]
license:
name: Apache 2.0
url: 'http://www.apache.org/licenses/LICENSE-2.0.html'
externalDocs:
description: |
Beacon project
url: 'http://beacon-project.io/'
paths: {}
components:
schemas:
LevelSeverity:
description: |
Level/severity ontology when and as applicable to phenotype observed. Value from TBD, e.g "mild".
type: string
enum:
- #TBD # Source TBD
example: 'severe'
DateOfOnset:
description: |
Date of onset/observation of phenotype, in (ISO8601 duration format).
type: string
example: 'P3Y6M4DT12H30M5S' #TBD to be confirmed
Disease:
description: |
Lisf of disease(s) been diagnosed to the individual, defined by diseaseID, age of onset,
stage, level of severity, outcome and the presence of family history.
type: object
properties:
diseaseId:
description: |
Disease identifier. Value from ICD10 disease codes or ontology terms
from disease ontologies such as HPO, OMIM, Orphanet, MONDO, e.g.
lactose intolerance (HP:0004789, ICD10CM:E73).
type: string
example:
- 'HP:0004789'
- 'ICD10CM:E73'
ageOfOnset:
$ref: 'https://raw.githubusercontent.com/ga4gh-beacon/specification-v2-default-schemas/master/common.yaml#/components/schemas/Age'
stage:
description: |
Ontology value from Ontology for General Medical Science or Disease
Stage Qualifier ontology (NCIT:C28108), e.g. acute onset (OGMS:0000119).
type: string
example: 'OGMS:0000119'
levelSeverity:
$ref: '#/components/schemas/LevelSeverity'
outcome:
description: |
Outcome of passed acute diseases. Value from TBD, eg. "fatal".
type: string
enum:
- TBD #TBD
example: 'fatal'
familyHistory:
description: |
Boolean indicating determined or self-reported presence of family
history of the disease.
type: boolean
example: True
Treatment:
description: |
List of treatment(s) been prescribed/administered to individual, defined by treatment ID), date and age of onset, dose, schedule and duration.
type: object
properties:
treatmentId:
description: |
Treatment ID. Value from TBD.
type: string
example: #TBD
treatmentRoute:
description: Route of treatment. Value from NCIT Route of Administration ontology.
type: string
dateAtOnset:
$ref: '#/components/schemas/DateOfOnset'
ageAtOnset:
$ref: 'https://raw.githubusercontent.com/ga4gh-beacon/specification-v2-default-schemas/master/common.yaml#/components/schemas/Age'
dose:
description: |
Treatment dose
type: integer
example: #TBD
units:
description: |
Treatment dose units
type: string
example: #TBD
schedule:
description: |
Treatment dose units
type: string
enum:
- #TBD
example: 'weekly'
duration:
description: |
Treatment duration in ISO8601 duration format
type: string
example: 'P32Y6M1D'
Intervention:
description: |
List of intervention(s) been practiced on subject,
defined by treatment ID, date and age of onset, dose,
schedule and duration.
type: object
properties:
interventionId:
description: |
Intervention ID. Value from Medical Action Ontology.
type: string
example: #TDB
date:
description: |
Date of intervention in ISO8601 duration format
type: string
example: 'P3Y6M4DT12H30M5S' #TBD to be confirmed
modifier:
description: Modifier of the intervention. Value from TBD.
type: string
ageAtIntervention:
$ref: 'https://raw.githubusercontent.com/ga4gh-beacon/specification-v2-default-schemas/master/common.yaml#/components/schemas/Age'
Pedigree:
description: |
Pedigree studie(s) in which the individual is part of.
type: object
properties:
pedigreeID:
description: |
Pedigree identifier.
type: string
example: 'Pedigree1001'
pedigreeDisease:
description: |
(disease code/ontology term object) Disease ID. Value from ICD10 disease
codes or ontology terms from disease ontologies such as HPO, OMIM, Orphanet, MONDO,
e.g. "lactose intolerance" (HP:0004789)
type: string
example: "HP:0004789"
pedigreeRole:
description: |
Pedigree role, defined as relationship to proband. Value from Family
member ontology (NCIT:C41256), e.g. "proband" (NCIT:C64435),
"identical twin" (NCIT:C73429), "mother" (NCIT:C25189).
type: string
example: 'ERO:0002041'
affectedStatus:
description: |
Affected status of Individual in disease of pedigree: "affected" or "unaffected".
type: string
enum:
- affected
- unaffected
numSubjects:
description: Number of subjects in pedigree.
type: integer
example: 10
PhenotypicFeature:
description: |
List of phenotypic feature(s) observed in the individual,
defined by phenotype, age of onset and level/ severity.
type: object
properties:
phenotypeId:
description: |
Phenotypic feature observed.
Value from Human Phenotype Ontology (HPO).
type: string
dateOfOnset:
description: |
Date of onset/observation of phenotype, in (ISO8601 duration format)
type: string
format: date
example: '2010-07-10'
onsetType:
description: Onset type. Value from HPO Onset ontology (HP:0003674), e.g. "congenital onset" (HP:0003577), "adult onset" (HP:0003581).
type: string
example: "HP:0003674"
ageOfOnset:
$ref: 'https://raw.githubusercontent.com/ga4gh-beacon/specification-v2-default-schemas/master/common.yaml#/components/schemas/Age'
levelSeverity:
$ref: '#/components/schemas/LevelSeverity'
Measure:
description: Measures(s) been taken from Individual, defined by measure ID, date and/or age at measure ment, unit and value.
type: object
properties:
measureId:
description: Measure ID. Value from Clinical Measurement ontology (CMO).
type: string
modifier:
description: Modifier of the measurement. Value from TBD.
type: string
date:
description: Date of intervention.
type: string
format: date
ageAtMeasure:
$ref: 'https://raw.githubusercontent.com/ga4gh-beacon/specification-v2-default-schemas/master/common.yaml#/components/schemas/Age'
Exposure:
description: |
Exposures(s) occurred to or practiced (lifestyle, behavioural exposures) by Individual,
defined by exposureID, date and age of onset, dose, schedule and duration.
type: object
properties:
exposureID:
description: Exposure ID. Value from Environment Exposure Ontology.
type: string
modifier:
description: Modifier of the exposure. Value from TBD.
type: string
date:
description: Date of the exposure.
type: string
format: date
ageAtExposure:
$ref: 'https://raw.githubusercontent.com/ga4gh-beacon/specification-v2-default-schemas/master/common.yaml#/components/schemas/Age'
Interactor:
description: |
Todo
type: object
properties:
relationType:
description: |
Ontology value for type of relation with Individual e.g "host", "pathogen", "commensal", etc
type: string
example: 'host'
individualId:
description: |
Individual identifier (external accession or internal ID).
type: string
example: P0001
datasetId:
description: Reference to dataset ID.
type: string
taxonId:
description: |
Taxon ID of Individual.
type: string
example: '9606'
sex:
description: |
Sex of the individual.
Value from NCIT General Qualifier (NCIT:C27993) ontology: UNKNOWN
(not assessed or not available) (NCIT:C17998), FEMALE (NCIT:C46113),
MALE, (NCIT:C46112) or OTHER SEX (NCIT:C45908).
type: string
enum:
- NCIT:C17998
- NCIT:C46113
- NCIT:C46112
- NCIT:C45908
example: 'NCIT:C17998'
ethnicity:
description: |
Ethnic background of the individual. Value from NCIT Race ontology
(NCIT:C17049), e.g. NCIT:C126531 (Latin American).
type: string
example: 'NCIT:C126531'
geographicOrigin:
description: |
Individual's country or region of origin (birthplace or residence
place regardless of ethnic origin). Value from GAZ Geographic
Location ontology (GAZ:00000448), e.g. GAZ:00002459 (United States
of America).
type: string
example: 'GAZ:00002459'
diseases:
description: |
List of disease(s) been diagnosed to the individual, defined by
disease ICD10 code, optionally other disease ontology ID(s), age of
onset, stage and the presence of family history.
type: array
items:
$ref: '#/components/schemas/Disease'
pedigrees:
type: array
items:
$ref: '#/components/schemas/Pedigree'
phenotypicFeatures:
type: array
items:
$ref: '#/components/schemas/PhenotypicFeature'
treatments:
type: array
items:
$ref: '#/components/schemas/Treatment'
interventions:
type: array
items:
$ref: '#/components/schemas/Intervention'
measures:
type: array
items:
$ref: '#/components/schemas/Measure'
exposures:
type: array
items:
$ref: '#/components/schemas/Exposure'
info:
description: |
Additional unspecified metadata about the dataset response or its
content.
type: object
example:
additionalInfoKey1:
- additionalInfoValue1
- additionalInfoValue2
additionalInfoKey2: additionalInfoValue3