Class: Human (HumanSubject)
A human subject in a study.
classDiagram
class HumanSubject
click HumanSubject href "../HumanSubject/"
AbstractSubject <|-- HumanSubject
click AbstractSubject href "../AbstractSubject/"
HumanSubject : additional_information
HumanSubject : age
HumanSubject : age_unit
HumanSubject --> "0..1" TimeUnits : age_unit
click TimeUnits href "../TimeUnits/"
HumanSubject : ancestry
HumanSubject --> "0..1" GeographicalLocations : ancestry
click GeographicalLocations href "../GeographicalLocations/"
HumanSubject : comorbidities
HumanSubject --> "*" Disease : comorbidities
click Disease href "../Disease/"
HumanSubject : ethnicity
HumanSubject : hlas
HumanSubject --> "*" HLAGenotype : hlas
click HLAGenotype href "../HLAGenotype/"
HumanSubject : sex
HumanSubject --> "0..1 _recommended_" BiologicalSex : sex
click BiologicalSex href "../BiologicalSex/"
HumanSubject : species
HumanSubject --> "1" HomoSapiens : species
click HomoSapiens href "../HomoSapiens/"
HumanSubject : study_id
HumanSubject : subject_id
HumanSubject : subject_type
HumanSubject --> "1" SubjectType : subject_type
click SubjectType href "../SubjectType/"
Inheritance
- AbstractSubject
- HumanSubject
Slots
| Name | Cardinality and Range | Description | Inheritance |
|---|---|---|---|
| age | 0..1 recommended Double |
The age of a subject at the "reference" timepoint (= when subject was include... | direct |
| age_unit | 0..1 TimeUnits |
The unit of the age value (e | direct |
| hlas | * HLAGenotype |
The HLA object | direct |
| comorbidities | * Disease |
The comorbidities of a human subject | direct |
| ancestry | 0..1 GeographicalLocations |
Broad geographic origin of ancestry (continent) | direct |
| ethnicity | 0..1 String |
The cultural or geographical group the subject belongs to | direct |
| subject_id | 1 String |
The user defined subject ID used to associate subject with samples | AbstractSubject |
| study_id | 1 String |
The internal identifier of the study | AbstractSubject |
| subject_type | 1 SubjectType |
Is the subject human, rodent, animal or a cell culture subject | AbstractSubject |
| species | 1 HomoSapiens |
The species of the subject | AbstractSubject |
| sex | 0..1 recommended BiologicalSex |
The biological sex of the subject | AbstractSubject |
| additional_information | 0..1 String |
Additional information related to this object | AbstractSubject |
Identifier and Mapping Information
Schema Source
- from schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
Mappings
| Mapping Type | Mapped Value |
|---|---|
| self | nfdi4immuno:HumanSubject |
| native | nfdi4immuno:HumanSubject |
LinkML Source
Direct
name: HumanSubject
description: A human subject in a study.
title: Human
from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
is_a: AbstractSubject
slots:
- age
- age_unit
- hlas
- comorbidities
- ancestry
- ethnicity
slot_usage:
species:
name: species
range: HomoSapiens
Induced
name: HumanSubject
description: A human subject in a study.
title: Human
from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
is_a: AbstractSubject
slot_usage:
species:
name: species
range: HomoSapiens
attributes:
age:
name: age
description: The age of a subject at the "reference" timepoint (= when subject
was included in the study).
title: Age
examples:
- value: '23.5'
from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
rank: 1000
alias: age
owner: HumanSubject
domain_of:
- HumanSubject
- NonHumanSubject
range: double
recommended: true
age_unit:
name: age_unit
description: The unit of the age value (e.g. year, day).
title: Age unit
examples:
- value: day
description: A period of 24 hours.
from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
rank: 1000
alias: age_unit
owner: HumanSubject
domain_of:
- HumanSubject
- NonHumanSubject
range: TimeUnits
hlas:
name: hlas
description: The HLA object.
title: HLA genotype
examples:
- value: '''[{"gene": {"key": "MRO:0000046", "term": "HLA-A gene"}, "allele":
"02", "protein": "101", "synonymous_variant": "01", "noncoding_variant": "02",
"expression_level": "N"}]''
'
description: HLA-A*02:101:01:02N.
from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
rank: 1000
alias: hlas
owner: HumanSubject
domain_of:
- HumanSubject
range: HLAGenotype
multivalued: true
comorbidities:
name: comorbidities
description: The comorbidities of a human subject.
title: Comorbidities
examples:
- value: '{"key": "icd10:C34", "term": "Malignant neoplasm of bronchus and lung"}'
- value: '{"key": "icd10:R50-R69", "term": "General symptoms and signs"}'
from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
rank: 1000
alias: comorbidities
owner: HumanSubject
domain_of:
- HumanSubject
range: Disease
multivalued: true
ancestry:
name: ancestry
description: Broad geographic origin of ancestry (continent).
title: Ancestry
examples:
- value: northern_africa
- value: central_america
from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
rank: 1000
alias: ancestry
owner: HumanSubject
domain_of:
- HumanSubject
range: GeographicalLocations
ethnicity:
name: ethnicity
description: The cultural or geographical group the subject belongs to.
title: Ethnicity
examples:
- value: Zapotec
description: Indigenous people of Mexico.
from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
rank: 1000
alias: ethnicity
owner: HumanSubject
domain_of:
- HumanSubject
range: string
subject_id:
name: subject_id
description: 'The user defined subject ID used to associate subject with samples.
Must be unique within the study.
'
title: Subject ID
examples:
- value: MH031
from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
rank: 1000
is_a: abstract_id
identifier: true
alias: subject_id
owner: HumanSubject
domain_of:
- Sample
- AbstractSubject
range: string
required: true
pattern: ^.+$
study_id:
name: study_id
description: The internal identifier of the study. Must be unique.
title: Study ID
examples:
- value: MS Study 01 UMKS
from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
rank: 1000
is_a: abstract_id
identifier: true
alias: study_id
owner: HumanSubject
domain_of:
- Study
- AbstractSubject
range: string
required: true
pattern: ^.+$
subject_type:
name: subject_type
description: Is the subject human, rodent, animal or a cell culture subject.
title: Subject Type
examples:
- value: human, rodent, other_animal, cell_culture
from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
rank: 1000
alias: subject_type
owner: HumanSubject
domain_of:
- AbstractSubject
range: SubjectType
required: true
pattern: .+
species:
name: species
description: The species of the subject.
title: Species
examples:
- value: '{''key'': ''NCBITaxon:9606'', ''term'': ''Homo sapiens''}'
from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
rank: 1000
alias: species
owner: HumanSubject
domain_of:
- AbstractSubject
range: HomoSapiens
required: true
pattern: .+
sex:
name: sex
description: The biological sex of the subject.
title: Sex
examples:
- value: Female
description: Female biological sex.
from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
rank: 1000
alias: sex
owner: HumanSubject
domain_of:
- AbstractSubject
range: BiologicalSex
recommended: true
additional_information:
name: additional_information
annotations:
preferred_format:
tag: preferred_format
value: json
description: 'Additional information related to this object. Can be in any format,
but JSON key-value pairs are preferred.
'
title: Additional information
from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
rank: 1000
alias: additional_information
owner: HumanSubject
domain_of:
- SampleEvent
- Sample
- Study
- AbstractSubject
range: string