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commonDefinitions.yaml
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commonDefinitions.yaml
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$schema: https://json-schema.org/draft/2020-12/schema
title: Common Definitions
description: Definitions for concepts used in several entry types, but that having
only one property are not complex enough to require a full independent schema document.
definitions:
Sex:
description: 'Sex of the individual. Recommended values from NCIT General Qualifier
(NCIT:C27993): "unknown" (not assessed or not available) - NCIT:C17998; "female"
- NCIT:C16576; "male" - NCIT:C20197'
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json
examples:
- id: NCIT:C16576
label: female
- id: NCIT:C20197
label: male
- id: NCIT:C1799
label: unknown
KaryotypicSex:
description: 'The chromosomal sex of an individual represented from a selection
of options. The values correspond to the ordinal values in the Phenopackets
schema where: 0 - UNKNOWN_KARYOTYPE (Untyped or inconclusive karyotyping); 1
- XX (Female); 2 - XY (Male); 3 - XO (Single X chromosome only); 4 - XXY (Two
X and one Y chromosome); 5 - XXX (Three X chromosomes); 6 - XXYY (Two X chromosomes
and two Y chromosomes); 7 - XXXY (Three X chromosomes and one Y chromosome);
8 - XXXX (Four X chromosomes); 9 - XYY (One X and two Y chromosomes); 10 - OTHER_KARYOTYPE
(None of the above types)'
$comments: Compares to https://github.com/phenopackets/phenopacket-schema/blob/master/docs/karyotypicsex.rst
type: string
enum:
- UNKNOWN_KARYOTYPE
- XX
- XY
- XO
- XXY
- XXX
- XXYY
- XXXY
- XXXX
- XYY
- OTHER_KARYOTYPE
default: UNKNOWN_KARYOTYPE
Timestamp:
description: Time in date-time ISO8601 string format.
type: string
format: date-time
examples:
- '1999-08-05T17:21:00+01:00'
- '2002-09-21T02:37:00-08:00'
Ethnicity:
description: Ethnic background of the individual. Recommended is the use of a
value from NCIT Race (NCIT:C17049) ontology term descendants, e.g. NCIT:C126531
(Latin American). A geographic ancestral origin category that is assigned to
a population group based mainly on physical characteristics that are thought
to be distinct and inherent. [ NCI ]
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json
examples:
- id: NCIT:C42331
label: African
- id: NCIT:C41260
label: Asian
- id: NCIT:C126535
label: Australian
- id: NCIT:C43851
label: European
- id: NCIT:C77812
label: North American
- id: NCIT:C126531
label: Latin American
- id: NCIT:C104495
label: Other race
GeographicLocation:
description: Country or region of origin of the individual (birthplace or residence
place regardless of ethnic origin). Value from GAZ Geographic Location ontology
(GAZ:00000448), e.g. GAZ:00002459 (United States of America).
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json
examples:
- id: GAZ:00002955
label: Slovenia
- id: GAZ:00002459
label: United States of America
- id: GAZ:00316959
label: Municipality of El Masnou
- id: GAZ:00000460
label: Eurasia
SeverityLevel:
description: 'Severity as applicable to phenotype or disease observed. Recommended
are values from Human Phenotype Ontology (HP:0012824), e.g `mild`. The intensity
or degree of a manifestation. Source: Phenopackets v2'
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json
examples:
- id: HP:0012828
label: Severe
- id: HP:0012829
label: Profound
- id: HP:0012826
label: Moderate
- id: HP:0012825
label: Mild
- id: HP:0012827
label: Borderline
Unit:
description: The kind of unit. Recommended from NCIT Unit of Category ontology
term (NCIT:C42568) descendants
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json
examples:
- id: NCIT:C70575
label: Roentgen
- id: NCIT:C28252
label: Kilogram
- id: NCIT:C28253
label: Milligram