Class: Aliquot (Aliquot)

A Portion of a sample extracted from a participant.

classDiagram class Aliquot click Aliquot href "../Aliquot/" HasExternalId <|-- Aliquot click HasExternalId href "../HasExternalId/" Aliquot : aliquot_id Aliquot : availability_status Aliquot --> "0..1" EnumSpecimenAvailability : availability_status click EnumSpecimenAvailability href "../EnumSpecimenAvailability/" Aliquot : concentration Aliquot : external_id Aliquot : sample_id Aliquot --> "1" Sample : sample_id click Sample href "../Sample/" Aliquot : volume Aliquot : volume_units

Inheritance

HasExternalId
- Aliquot

Slots

Name	Cardinality and Range	Description	Inheritance
aliquot_id	1 String	Aliquot Global ID	direct
availability_status	0..1 EnumSpecimenAvailability	Can this Sample be requested for further analysis?	direct
volume	0..1 Float	What is the volume of the Aliquot?	direct
volume_units	0..1 Uriorcurie	Units associated with the volume (ucum)	direct
concentration	0..1 Uriorcurie	What is the concentration of the analyte in the Aliquot?	direct
sample_id	1 Sample	Sample Global ID	direct
external_id	* Uriorcurie	Other identifiers for this entity, eg, from the submitting study or in system...	HasExternalId

Identifier and Mapping Information

Annotations

property	value
fhir_resource	Specimen
fhir_profile	https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-sample
fhir_element	container

Schema Source

from schema: https://carrollaboratory.github.io/kfi-fhir-input

Mappings

Mapping Type	Mapped Value
self	kfi_fhir_sparks:Aliquot
native	kfi_fhir_sparks:Aliquot

LinkML Source

Direct

name: Aliquot
annotations:
  fhir_resource:
    tag: fhir_resource
    value: Specimen
  fhir_profile:
    tag: fhir_profile
    value: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-sample
  fhir_element:
    tag: fhir_element
    value: container
description: A Portion of a sample extracted from a participant.
title: Aliquot
from_schema: https://carrollaboratory.github.io/kfi-fhir-input
is_a: HasExternalId
slots:
- aliquot_id
- availability_status
- volume
- volume_units
- concentration
- sample_id
slot_usage:
  aliquot_id:
    name: aliquot_id
    identifier: true
    range: string
    required: true
  sample_id:
    name: sample_id
    identifier: false
    required: true

Induced

name: Aliquot
annotations:
  fhir_resource:
    tag: fhir_resource
    value: Specimen
  fhir_profile:
    tag: fhir_profile
    value: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-sample
  fhir_element:
    tag: fhir_element
    value: container
description: A Portion of a sample extracted from a participant.
title: Aliquot
from_schema: https://carrollaboratory.github.io/kfi-fhir-input
is_a: HasExternalId
slot_usage:
  aliquot_id:
    name: aliquot_id
    identifier: true
    range: string
    required: true
  sample_id:
    name: sample_id
    identifier: false
    required: true
attributes:
  aliquot_id:
    name: aliquot_id
    description: Aliquot Global ID
    title: aliquot ID
    from_schema: https://carrollaboratory.github.io/kfi-fhir-input
    rank: 1000
    identifier: true
    alias: aliquot_id
    owner: Aliquot
    domain_of:
    - Aliquot
    range: string
    required: true
  availability_status:
    name: availability_status
    annotations:
      fhir_resource:
        tag: fhir_resource
        value: Specimen
      fhir_profile:
        tag: fhir_profile
        value: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-sample
      fhir_element:
        tag: fhir_element
        value: extension[AliquotAvailability].valueCode
    description: Can this Sample be requested for further analysis?
    title: Availability Status
    from_schema: https://carrollaboratory.github.io/kfi-fhir-input
    rank: 1000
    alias: availability_status
    owner: Aliquot
    domain_of:
    - Sample
    - Aliquot
    range: EnumSpecimenAvailability
    required: false
    multivalued: false
  volume:
    name: volume
    annotations:
      fhir_profile:
        tag: fhir_profile
        value: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-participant-assertion
      fhir_element:
        tag: fhir_element
        value: collection[].quantity.value
      fhir_resource:
        tag: fhir_resource
        value: Specimen
    description: What is the volume of the Aliquot?
    title: Volume
    from_schema: https://carrollaboratory.github.io/kfi-fhir-input
    rank: 1000
    alias: volume
    owner: Aliquot
    domain_of:
    - Aliquot
    range: float
    required: false
    multivalued: false
  volume_units:
    name: volume_units
    annotations:
      fhir_profile:
        tag: fhir_profile
        value: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-participant-assertion
      fhir_element:
        tag: fhir_element
        value: collection[].quantity.unit
      fhir_resource:
        tag: fhir_resource
        value: Specimen
    description: Units associated with the volume (ucum)
    title: Volume Units
    from_schema: https://carrollaboratory.github.io/kfi-fhir-input
    rank: 1000
    alias: volume_units
    owner: Aliquot
    domain_of:
    - Aliquot
    range: uriorcurie
    required: false
    multivalued: false
  concentration:
    name: concentration
    annotations:
      fhir_profile:
        tag: fhir_profile
        value: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-participant-assertion
      fhir_element:
        tag: fhir_element
        value: collection[].extension[AliquotConcentration].valueQuantity.value
      fhir_resource:
        tag: fhir_resource
        value: Specimen
    description: What is the concentration of the analyte in the Aliquot?
    title: Concentration
    from_schema: https://carrollaboratory.github.io/kfi-fhir-input
    rank: 1000
    alias: concentration
    owner: Aliquot
    domain_of:
    - Aliquot
    range: uriorcurie
    required: false
    multivalued: false
  sample_id:
    name: sample_id
    description: Sample Global ID
    title: Sample ID
    from_schema: https://carrollaboratory.github.io/kfi-fhir-input
    rank: 1000
    identifier: false
    alias: sample_id
    owner: Aliquot
    domain_of:
    - Participant
    - Sample
    - Aliquot
    range: Sample
    required: true
    multivalued: false
  external_id:
    name: external_id
    description: Other identifiers for this entity, eg, from the submitting study
      or in systems link dbGaP
    title: External Identifiers
    from_schema: https://carrollaboratory.github.io/kfi-fhir-input
    rank: 1000
    alias: external_id
    owner: Aliquot
    domain_of:
    - HasExternalId
    range: uriorcurie
    required: false
    multivalued: true