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Class: Sample (Sample)

Sample encompasses biospecimen collection, sample information, and aliquot information.

URI: kfi_fhir_sparks:Sample

classDiagram class Sample click Sample href "../Sample/" HasExternalId <|-- Sample click HasExternalId href "../HasExternalId/" Sample : age_at_collection Sample --> "0..1" AgeAt : age_at_collection click AgeAt href "../AgeAt/" Sample : availability_status Sample --> "0..1" EnumSpecimenAvailability : availability_status click EnumSpecimenAvailability href "../EnumSpecimenAvailability/" Sample : collection_method Sample : collection_site Sample : external_id Sample : laterality Sample : parent_sample_id Sample --> "0..1" Sample : parent_sample_id click Sample href "../Sample/" Sample : participant_id Sample --> "1" Participant : participant_id click Participant href "../Participant/" Sample : processing Sample : quantity Sample : quantity_units Sample : sample_id Sample : sample_type Sample : spatial_qualifier Sample : storage_method

Inheritance

Slots

Name Cardinality and Range Description Inheritance
sample_id 1
String		 Sample Global ID direct
parent_sample_id 0..1
Sample		 Sample Global ID associated with the parent sample direct
participant_id 1
Participant		 The Global ID for the Participant direct
sample_type 1
Uriorcurie		 The type of material of which this Sample is comprised direct
age_at_collection 0..1
AgeAt		 The age at which this biospecimen was collected direct
collection_method 0..1
Uriorcurie		 The approach used to collect the biospecimen ([LOINC](https://loinc direct
collection_site 0..1
Uriorcurie		 The location of the specimen collection direct
spatial_qualifier 0..1
Uriorcurie		 Any spatial/location qualifiers direct
laterality 0..1
Uriorcurie		 Laterality information for the site direct
processing *
Uriorcurie		 Processing that was applied to the Parent Sample or from the Biospecimen Coll... direct
availability_status 0..1
EnumSpecimenAvailability		 Can this Sample be requested for further analysis? direct
storage_method 0..1
Uriorcurie		 How is the Sample stored, eg, Frozen or with additives (e direct
quantity 0..1
Float		 The total quantity of the specimen direct
quantity_units 0..1
Uriorcurie		 Units associated with the quantity (ucum) direct
external_id *
Uriorcurie		 Other identifiers for this entity, eg, from the submitting study or in system... HasExternalId

Usages

used by used in type used
Participant sample_id range Sample
Sample parent_sample_id range Sample
Aliquot sample_id range Sample
FileMetaData samples range Sample

Identifier and Mapping Information

Annotations

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

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Sample
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
description: Sample encompasses biospecimen collection, sample information, and aliquot
  information.
title: Sample
from_schema: https://carrollaboratory.github.io/kfi-fhir-input
is_a: HasExternalId
slots:
- sample_id
- parent_sample_id
- participant_id
- sample_type
- age_at_collection
- collection_method
- collection_site
- spatial_qualifier
- laterality
- processing
- availability_status
- storage_method
- quantity
- quantity_units
slot_usage:
  sample_id:
    name: sample_id
    identifier: true
    range: string
    required: true

Induced

name: Sample
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
description: Sample encompasses biospecimen collection, sample information, and aliquot
  information.
title: Sample
from_schema: https://carrollaboratory.github.io/kfi-fhir-input
is_a: HasExternalId
slot_usage:
  sample_id:
    name: sample_id
    identifier: true
    range: string
    required: true
attributes:
  sample_id:
    name: sample_id
    description: Sample Global ID
    title: Sample ID
    from_schema: https://carrollaboratory.github.io/kfi-fhir-input
    rank: 1000
    identifier: true
    alias: sample_id
    owner: Sample
    domain_of:
    - Participant
    - Sample
    - Aliquot
    range: string
    required: true
    multivalued: false
  parent_sample_id:
    name: parent_sample_id
    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: parent
    description: Sample Global ID associated with the parent sample
    title: Parent Sample ID
    from_schema: https://carrollaboratory.github.io/kfi-fhir-input
    rank: 1000
    alias: parent_sample_id
    owner: Sample
    domain_of:
    - Sample
    range: Sample
    required: false
    multivalued: false
  participant_id:
    name: participant_id
    description: The Global ID for the Participant
    title: Participant ID
    from_schema: https://carrollaboratory.github.io/kfi-fhir-input
    rank: 1000
    alias: participant_id
    owner: Sample
    domain_of:
    - ParticipantAssertion
    - Participant
    - Person
    - StudyMembership
    - Sample
    - NCPIFile
    range: Participant
    required: true
  sample_type:
    name: sample_type
    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: type
    description: The type of material of which this Sample is comprised
    title: Sample Type
    from_schema: https://carrollaboratory.github.io/kfi-fhir-input
    rank: 1000
    alias: sample_type
    owner: Sample
    domain_of:
    - Sample
    range: uriorcurie
    required: true
    multivalued: false
  age_at_collection:
    name: age_at_collection
    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: collectedDateTime
    description: The age at which this biospecimen was collected. Could be expressed
      with a term, an age, or an age range.
    title: Age at Collection
    from_schema: https://carrollaboratory.github.io/kfi-fhir-input
    rank: 1000
    alias: age_at_collection
    owner: Sample
    domain_of:
    - Sample
    range: AgeAt
    required: false
    multivalued: false
  collection_method:
    name: collection_method
    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: collection.method
    description: The approach used to collect the biospecimen ([LOINC](https://loinc.org))
    title: Collection Method
    from_schema: https://carrollaboratory.github.io/kfi-fhir-input
    rank: 1000
    alias: collection_method
    owner: Sample
    domain_of:
    - Sample
    range: uriorcurie
    required: false
    multivalued: false
  collection_site:
    name: collection_site
    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: bodySite
    description: The location of the specimen collection
    title: Collection Site
    from_schema: https://carrollaboratory.github.io/kfi-fhir-input
    rank: 1000
    alias: collection_site
    owner: Sample
    domain_of:
    - Sample
    range: uriorcurie
    required: false
    multivalued: false
  spatial_qualifier:
    name: spatial_qualifier
    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: collection.extension[biospecimenSpatial]
    description: Any spatial/location qualifiers
    title: Spatial Qualifier
    from_schema: https://carrollaboratory.github.io/kfi-fhir-input
    rank: 1000
    alias: spatial_qualifier
    owner: Sample
    domain_of:
    - Sample
    range: uriorcurie
    required: false
    multivalued: false
  laterality:
    name: laterality
    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: collection.extension[biospecimenLaterality]
    description: Laterality information for the site
    title: Laterality
    from_schema: https://carrollaboratory.github.io/kfi-fhir-input
    rank: 1000
    alias: laterality
    owner: Sample
    domain_of:
    - Sample
    range: uriorcurie
    required: false
    multivalued: false
  processing:
    name: processing
    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: processing[].procedure
    description: Processing that was applied to the Parent Sample or from the Biospecimen
      Collection that yielded this distinct sample
    title: Processing
    from_schema: https://carrollaboratory.github.io/kfi-fhir-input
    rank: 1000
    alias: processing
    owner: Sample
    domain_of:
    - Sample
    range: uriorcurie
    required: false
    multivalued: 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: Sample
    domain_of:
    - Sample
    - Aliquot
    range: EnumSpecimenAvailability
    required: false
    multivalued: false
  storage_method:
    name: storage_method
    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: condition
    description: How is the Sample stored, eg, Frozen or with additives (e.g. https://terminology.hl7.org/5.3.0/ValueSet-v2-0493.html)
    title: Storage Method
    from_schema: https://carrollaboratory.github.io/kfi-fhir-input
    rank: 1000
    alias: storage_method
    owner: Sample
    domain_of:
    - Sample
    range: uriorcurie
    required: false
    multivalued: false
  quantity:
    name: quantity
    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: collection[].quantity
    description: The total quantity of the specimen
    title: Quantity
    from_schema: https://carrollaboratory.github.io/kfi-fhir-input
    rank: 1000
    alias: quantity
    owner: Sample
    domain_of:
    - Sample
    range: float
    required: false
    multivalued: false
  quantity_units:
    name: quantity_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: collection[].quantity.units
    description: Units associated with the quantity (ucum)
    title: Quantity Units
    from_schema: https://carrollaboratory.github.io/kfi-fhir-input
    rank: 1000
    alias: quantity_units
    owner: Sample
    domain_of:
    - Sample
    range: uriorcurie
    required: false
    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: Sample
    domain_of:
    - HasExternalId
    range: uriorcurie
    required: false
    multivalued: true