Class: Biosample

A Biosample refers to a unit of biological material from which the substrate molecules (e.g. genomic DNA, RNA, proteins) for molecular analyses (e.g. sequencing, array hybridisation, mass-spectrometry) are extracted. Examples would be a tissue biopsy, a single cell from a culture for single cell genome sequencing or a protein fraction from a gradient centrifugation. Several instances (e.g. technical replicates) or types of experiments (e.g. genomic array as well as RNA-seq experiments) may refer to the same Biosample. FHIR mapping: Specimen (http://www.hl7.org/fhir/specimen.html).

URI: phenopackets:Biosample

erDiagram Biosample { string derivedFromId string description string id string individualId } OntologyClass { string id string label } TimeElement { string timestamp } TimeInterval { string end string start } GestationalAge { integer days integer weeks } AgeRange { } Age { string iso8601duration } Procedure { } PhenotypicFeature { string description boolean excluded } Evidence { } Measurement { string description } Value { } ComplexValue { } File { string uri } Dictionary { } Biosample ||--}o OntologyClass : "diagnosticMarkers" Biosample ||--}o File : "files" Biosample ||--|o OntologyClass : "histologicalDiagnosis" Biosample ||--|o OntologyClass : "materialSample" Biosample ||--}o Measurement : "measurements" Biosample ||--|o OntologyClass : "pathologicalStage" Biosample ||--}o OntologyClass : "pathologicalTnmFinding" Biosample ||--}o PhenotypicFeature : "phenotypicFeatures" Biosample ||--|o Procedure : "procedure" Biosample ||--|o OntologyClass : "sampleProcessing" Biosample ||--|o OntologyClass : "sampleStorage" Biosample ||--|o OntologyClass : "sampleType" Biosample ||--|o OntologyClass : "sampledTissue" Biosample ||--|o OntologyClass : "taxonomy" Biosample ||--|o TimeElement : "timeOfCollection" Biosample ||--|o OntologyClass : "tumorGrade" Biosample ||--|o OntologyClass : "tumorProgression" TimeElement ||--|o Age : "age" TimeElement ||--|o AgeRange : "ageRange" TimeElement ||--|o GestationalAge : "gestationalAge" TimeElement ||--|o TimeInterval : "interval" TimeElement ||--|o OntologyClass : "ontologyClass" AgeRange ||--|o Age : "end" AgeRange ||--|o Age : "start" Procedure ||--|o OntologyClass : "bodySite" Procedure ||--|o OntologyClass : "code" Procedure ||--|o TimeElement : "performed" PhenotypicFeature ||--}o Evidence : "evidence" PhenotypicFeature ||--}o OntologyClass : "modifiers" PhenotypicFeature ||--|o TimeElement : "onset" PhenotypicFeature ||--|o TimeElement : "resolution" PhenotypicFeature ||--|o OntologyClass : "severity" PhenotypicFeature ||--|o OntologyClass : "type" Evidence ||--|o OntologyClass : "evidenceCode" Evidence ||--|o ExternalReference : "reference" Measurement ||--|o OntologyClass : "assay" Measurement ||--|o ComplexValue : "complexValue" Measurement ||--|o Procedure : "procedure" Measurement ||--|o TimeElement : "timeObserved" Measurement ||--|o Value : "value" Value ||--|o OntologyClass : "ontologyClass" Value ||--|o Quantity : "quantity" ComplexValue ||--}o TypedQuantity : "typedQuantities" File ||--|o Dictionary : "fileAttributes" File ||--|o Dictionary : "individualToFileIdentifiers"

Slots

Name	Cardinality and Range	Description	Inheritance
derivedFromId	0..1 String	The id of the parent biosample this biosample was derived from	direct
description	0..1 String	The biosample's description	direct
diagnosticMarkers	0..* OntologyClass	Clinically relevant bio markers	direct
files	0..* File	Pointer to the relevant file(s) for the biosample	direct
histologicalDiagnosis	0..1 OntologyClass	This is the pathologist’s diagnosis and may often represent a refinement of t...	direct
id	0..1 String	biosamples SAMN08666232 Human Cell Atlas The Biosample id This is unique in t...	direct
individualId	0..1 String	The id of the individual this biosample was derived from	direct
materialSample	0..1 OntologyClass	This element can be used to specify the status of the sample	direct
measurements	0..* Measurement		direct
pathologicalStage	0..1 OntologyClass	ARGO mapping specimen::pathological_tumour_staging_system ARGO mapping specim...	direct
pathologicalTnmFinding	0..* OntologyClass	ARGO mapping specimen::pathological_t_category ARGO mapping specimen::patholo...	direct
phenotypicFeatures	0..* PhenotypicFeature	Phenotypic characteristics of the BioSample, for example histological finding...	direct
procedure	0..1 Procedure	Clinical procedure performed on the subject in order to extract the biosample	direct
sampleProcessing	0..1 OntologyClass	Field to represent how the sample was processed	direct
sampleStorage	0..1 OntologyClass	Field to represent how the sample was stored ARGO mapping specimen::specimen_...	direct
sampleType	0..1 OntologyClass	Recommended use of EFO term to describe the sample	direct
sampledTissue	0..1 OntologyClass	UBERON class describing the tissue from which the specimen was collected	direct
taxonomy	0..1 OntologyClass	NCBI taxonomic identifier (NCBITaxon) of the sample e	direct
timeOfCollection	0..1 TimeElement	An TimeElement describing either the age of the individual this biosample was...	direct
tumorGrade	0..1 OntologyClass	Potentially a child term of NCIT:C28076 (Disease Grade Qualifier) or equivale...	direct
tumorProgression	0..1 OntologyClass	Is the specimen tissue from the primary tumor, a metastasis or a recurrence? ...	direct

Usages

used by	used in	type	used
Phenopacket	biosamples	range	Biosample

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/linkml/phenopackets/phenopackets

Mappings

Mapping Type	Mapped Value
self	phenopackets:Biosample
native	phenopackets:Biosample

LinkML Source

Direct

name: Biosample
description: 'A Biosample refers to a unit of biological material from which the substrate
  molecules (e.g. genomic DNA, RNA, proteins) for molecular analyses (e.g. sequencing,
  array hybridisation, mass-spectrometry) are extracted. Examples would be a tissue
  biopsy, a single cell from a culture for single cell genome sequencing or a protein
  fraction from a gradient centrifugation. Several instances (e.g. technical replicates)
  or types of experiments (e.g. genomic array as well as RNA-seq experiments) may
  refer to the same Biosample. FHIR mapping: Specimen (http://www.hl7.org/fhir/specimen.html).'
from_schema: https://w3id.org/linkml/phenopackets/phenopackets
attributes:
  derivedFromId:
    name: derivedFromId
    annotations:
      rank:
        tag: rank
        value: 3
    description: The id of the parent biosample this biosample was derived from.
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - Biosample
    range: string
  description:
    name: description
    annotations:
      rank:
        tag: rank
        value: 4
    description: The biosample's description. This attribute contains human readable
      text. The "description" attributes should not contain any structured data.
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    domain_of:
    - Cohort
    - ExternalReference
    - Measurement
    - PhenotypicFeature
    - Biosample
    - GeneDescriptor
    - VariationDescriptor
    range: string
  diagnosticMarkers:
    name: diagnosticMarkers
    annotations:
      rank:
        tag: rank
        value: 16
    description: Clinically relevant bio markers. Most of the assays such as IHC are
      covered by the NCIT under the sub-hierarchy NCIT:C25294 (Laboratory Procedure).
      e.g. NCIT:C68748 (HER2/Neu Positive), NCIT:C131711 (Human Papillomavirus-18
      Positive)
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    multivalued: true
    domain_of:
    - Biosample
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  files:
    name: files
    annotations:
      rank:
        tag: rank
        value: 18
    description: Pointer to the relevant file(s) for the biosample. Files relating
      to the entire individual e.g. a germline exome/genome should be associated with
      the Phenopacket rather than the Biosample it was derived from.
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    multivalued: true
    domain_of:
    - Cohort
    - Family
    - Phenopacket
    - Biosample
    range: File
    inlined: true
    inlined_as_list: true
  histologicalDiagnosis:
    name: histologicalDiagnosis
    annotations:
      rank:
        tag: rank
        value: 11
    description: This is the pathologist’s diagnosis and may often represent a refinement
      of the clinical diagnosis given in the Patient/Clinical module. Should use the
      same terminology as diagnosis, but represent the pathologist’s findings. Normal
      samples would be tagged with the term "NCIT:C38757", "Negative Finding" ARGO
      mapping specimen::tumour_histological_type
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    exact_mappings:
    - ARGO:specimen.tumour_histological_type
    rank: 1000
    domain_of:
    - Biosample
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  id:
    name: id
    annotations:
      percent_encoded:
        tag: percent_encoded
        value: true
      rank:
        tag: rank
        value: 1
    description: biosamples SAMN08666232 Human Cell Atlas The Biosample id This is
      unique in the context of the server instance. ARGO mapping specimen::submitter_specimen_id
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    exact_mappings:
    - ARGO:specimen.submitter_specimen_id
    domain_of:
    - Cohort
    - Family
    - Phenopacket
    - ExternalReference
    - OntologyClass
    - Biosample
    - Allele
    - ChromosomeLocation
    - CopyNumber
    - Member
    - SequenceLocation
    - Text
    - VariationDescriptor
    - VcfRecord
    - Interpretation
    - Individual
    - Resource
    range: string
  individualId:
    name: individualId
    annotations:
      rank:
        tag: rank
        value: 2
    description: The id of the individual this biosample was derived from. ARGO mapping
      specimen::submitter_donor_id
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    exact_mappings:
    - ARGO:specimen.submitter_donor_id
    rank: 1000
    domain_of:
    - Biosample
    - Person
    range: string
  materialSample:
    name: materialSample
    annotations:
      rank:
        tag: rank
        value: 19
    description: 'This element can be used to specify the status of the sample. For
      instance, a status may be used as a normal control, often in combination with
      another sample that is thought to contain a pathological finding. We recommend
      use of ontology terms such as: EFO:0009654 (reference sample) or EFO:0009655
      (abnormal sample) ARGO mapping sample_registration::tumour_normal_designation'
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    exact_mappings:
    - ARGO:sample_registration.tumour_normal_designation
    rank: 1000
    domain_of:
    - Biosample
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  measurements:
    name: measurements
    annotations:
      rank:
        tag: rank
        value: 8
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    multivalued: true
    domain_of:
    - Phenopacket
    - Biosample
    range: Measurement
    inlined: true
    inlined_as_list: true
  pathologicalStage:
    name: pathologicalStage
    annotations:
      rank:
        tag: rank
        value: 14
    description: ARGO mapping specimen::pathological_tumour_staging_system ARGO mapping
      specimen::pathological_stage_group
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    exact_mappings:
    - ARGO:specimen.pathological_tumour_staging_system
    rank: 1000
    domain_of:
    - Biosample
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  pathologicalTnmFinding:
    name: pathologicalTnmFinding
    annotations:
      rank:
        tag: rank
        value: 15
    description: ARGO mapping specimen::pathological_t_category ARGO mapping specimen::pathological_n_category
      ARGO mapping specimen::pathological_m_category
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    exact_mappings:
    - ARGO:specimen.pathological_t_category
    rank: 1000
    multivalued: true
    domain_of:
    - Biosample
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  phenotypicFeatures:
    name: phenotypicFeatures
    annotations:
      rank:
        tag: rank
        value: 7
    description: Phenotypic characteristics of the BioSample, for example histological
      findings of a biopsy.
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    multivalued: true
    domain_of:
    - Phenopacket
    - Biosample
    range: PhenotypicFeature
    inlined: true
    inlined_as_list: true
  procedure:
    name: procedure
    annotations:
      rank:
        tag: rank
        value: 17
    description: Clinical procedure performed on the subject in order to extract the
      biosample. ARGO mapping specimen::specimen_anatomic_location - Procedure::body_site
      ARGO mapping specimen::specimen_acquisition_interval - Procedure::time_performed
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    exact_mappings:
    - ARGO:specimen.specimen_anatomic_location
    domain_of:
    - Measurement
    - Biosample
    - MedicalAction
    range: Procedure
  sampleProcessing:
    name: sampleProcessing
    annotations:
      rank:
        tag: rank
        value: 20
    description: Field to represent how the sample was processed. ARGO mapping specimen::specimen_processing
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    exact_mappings:
    - ARGO:specimen.specimen_processing
    rank: 1000
    domain_of:
    - Biosample
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  sampleStorage:
    name: sampleStorage
    annotations:
      rank:
        tag: rank
        value: 21
    description: Field to represent how the sample was stored ARGO mapping specimen::specimen_storage
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    exact_mappings:
    - ARGO:specimen.specimen_storage
    rank: 1000
    domain_of:
    - Biosample
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  sampleType:
    name: sampleType
    annotations:
      rank:
        tag: rank
        value: 6
    description: Recommended use of EFO term to describe the sample. e.g. Amplified
      DNA, ctDNA, Total RNA, Lung tissue, Cultured cells... ARGO mapping sample_registration::sample_type
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    exact_mappings:
    - ARGO:sample_registration.sample_type
    rank: 1000
    domain_of:
    - Biosample
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  sampledTissue:
    name: sampledTissue
    annotations:
      rank:
        tag: rank
        value: 5
    description: 'UBERON class describing the tissue from which the specimen was collected.
      PDX-MI mapping: ''Specimen tumor tissue'' FHIR mapping: Specimen.type ARGO mapping
      sample_registration::specimen_tissue_source'
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    exact_mappings:
    - ARGO:sample_registration.specimen_tissue_source
    rank: 1000
    domain_of:
    - Biosample
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  taxonomy:
    name: taxonomy
    annotations:
      rank:
        tag: rank
        value: 9
    description: NCBI taxonomic identifier (NCBITaxon) of the sample e.g. NCBITaxon:9606
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - Biosample
    - Individual
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  timeOfCollection:
    name: timeOfCollection
    annotations:
      rank:
        tag: rank
        value: 10
    description: An TimeElement describing either the age of the individual this biosample
      was derived from at the time of collection, or the time itself. See http://build.fhir.org/datatypes
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - Biosample
    range: TimeElement
    inlined: true
    inlined_as_list: true
  tumorGrade:
    name: tumorGrade
    annotations:
      rank:
        tag: rank
        value: 13
    description: Potentially a child term of NCIT:C28076 (Disease Grade Qualifier)
      or equivalent See https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - Biosample
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  tumorProgression:
    name: tumorProgression
    annotations:
      rank:
        tag: rank
        value: 12
    description: Is the specimen tissue from the primary tumor, a metastasis or a
      recurrence? Most likely a child term of NCIT:C7062 (Neoplasm by Special Category)
      NCIT:C3677 (Benign Neoplasm) NCIT:C84509 (Primary Malignant Neoplasm) NCIT:C95606
      (Second Primary Malignant Neoplasm) NCIT:C3261 (Metastatic Neoplasm) NCIT:C4813
      (Recurrent Malignant Neoplasm)
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - Biosample
    range: OntologyClass
    inlined: true
    inlined_as_list: true

Induced

name: Biosample
description: 'A Biosample refers to a unit of biological material from which the substrate
  molecules (e.g. genomic DNA, RNA, proteins) for molecular analyses (e.g. sequencing,
  array hybridisation, mass-spectrometry) are extracted. Examples would be a tissue
  biopsy, a single cell from a culture for single cell genome sequencing or a protein
  fraction from a gradient centrifugation. Several instances (e.g. technical replicates)
  or types of experiments (e.g. genomic array as well as RNA-seq experiments) may
  refer to the same Biosample. FHIR mapping: Specimen (http://www.hl7.org/fhir/specimen.html).'
from_schema: https://w3id.org/linkml/phenopackets/phenopackets
attributes:
  derivedFromId:
    name: derivedFromId
    annotations:
      rank:
        tag: rank
        value: 3
    description: The id of the parent biosample this biosample was derived from.
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: derivedFromId
    owner: Biosample
    domain_of:
    - Biosample
    range: string
  description:
    name: description
    annotations:
      rank:
        tag: rank
        value: 4
    description: The biosample's description. This attribute contains human readable
      text. The "description" attributes should not contain any structured data.
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    alias: description
    owner: Biosample
    domain_of:
    - Cohort
    - ExternalReference
    - Measurement
    - PhenotypicFeature
    - Biosample
    - GeneDescriptor
    - VariationDescriptor
    range: string
  diagnosticMarkers:
    name: diagnosticMarkers
    annotations:
      rank:
        tag: rank
        value: 16
    description: Clinically relevant bio markers. Most of the assays such as IHC are
      covered by the NCIT under the sub-hierarchy NCIT:C25294 (Laboratory Procedure).
      e.g. NCIT:C68748 (HER2/Neu Positive), NCIT:C131711 (Human Papillomavirus-18
      Positive)
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    multivalued: true
    alias: diagnosticMarkers
    owner: Biosample
    domain_of:
    - Biosample
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  files:
    name: files
    annotations:
      rank:
        tag: rank
        value: 18
    description: Pointer to the relevant file(s) for the biosample. Files relating
      to the entire individual e.g. a germline exome/genome should be associated with
      the Phenopacket rather than the Biosample it was derived from.
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    multivalued: true
    alias: files
    owner: Biosample
    domain_of:
    - Cohort
    - Family
    - Phenopacket
    - Biosample
    range: File
    inlined: true
    inlined_as_list: true
  histologicalDiagnosis:
    name: histologicalDiagnosis
    annotations:
      rank:
        tag: rank
        value: 11
    description: This is the pathologist’s diagnosis and may often represent a refinement
      of the clinical diagnosis given in the Patient/Clinical module. Should use the
      same terminology as diagnosis, but represent the pathologist’s findings. Normal
      samples would be tagged with the term "NCIT:C38757", "Negative Finding" ARGO
      mapping specimen::tumour_histological_type
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    exact_mappings:
    - ARGO:specimen.tumour_histological_type
    rank: 1000
    alias: histologicalDiagnosis
    owner: Biosample
    domain_of:
    - Biosample
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  id:
    name: id
    annotations:
      percent_encoded:
        tag: percent_encoded
        value: true
      rank:
        tag: rank
        value: 1
    description: biosamples SAMN08666232 Human Cell Atlas The Biosample id This is
      unique in the context of the server instance. ARGO mapping specimen::submitter_specimen_id
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    exact_mappings:
    - ARGO:specimen.submitter_specimen_id
    alias: id
    owner: Biosample
    domain_of:
    - Cohort
    - Family
    - Phenopacket
    - ExternalReference
    - OntologyClass
    - Biosample
    - Allele
    - ChromosomeLocation
    - CopyNumber
    - Member
    - SequenceLocation
    - Text
    - VariationDescriptor
    - VcfRecord
    - Interpretation
    - Individual
    - Resource
    range: string
  individualId:
    name: individualId
    annotations:
      rank:
        tag: rank
        value: 2
    description: The id of the individual this biosample was derived from. ARGO mapping
      specimen::submitter_donor_id
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    exact_mappings:
    - ARGO:specimen.submitter_donor_id
    rank: 1000
    alias: individualId
    owner: Biosample
    domain_of:
    - Biosample
    - Person
    range: string
  materialSample:
    name: materialSample
    annotations:
      rank:
        tag: rank
        value: 19
    description: 'This element can be used to specify the status of the sample. For
      instance, a status may be used as a normal control, often in combination with
      another sample that is thought to contain a pathological finding. We recommend
      use of ontology terms such as: EFO:0009654 (reference sample) or EFO:0009655
      (abnormal sample) ARGO mapping sample_registration::tumour_normal_designation'
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    exact_mappings:
    - ARGO:sample_registration.tumour_normal_designation
    rank: 1000
    alias: materialSample
    owner: Biosample
    domain_of:
    - Biosample
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  measurements:
    name: measurements
    annotations:
      rank:
        tag: rank
        value: 8
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    multivalued: true
    alias: measurements
    owner: Biosample
    domain_of:
    - Phenopacket
    - Biosample
    range: Measurement
    inlined: true
    inlined_as_list: true
  pathologicalStage:
    name: pathologicalStage
    annotations:
      rank:
        tag: rank
        value: 14
    description: ARGO mapping specimen::pathological_tumour_staging_system ARGO mapping
      specimen::pathological_stage_group
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    exact_mappings:
    - ARGO:specimen.pathological_tumour_staging_system
    rank: 1000
    alias: pathologicalStage
    owner: Biosample
    domain_of:
    - Biosample
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  pathologicalTnmFinding:
    name: pathologicalTnmFinding
    annotations:
      rank:
        tag: rank
        value: 15
    description: ARGO mapping specimen::pathological_t_category ARGO mapping specimen::pathological_n_category
      ARGO mapping specimen::pathological_m_category
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    exact_mappings:
    - ARGO:specimen.pathological_t_category
    rank: 1000
    multivalued: true
    alias: pathologicalTnmFinding
    owner: Biosample
    domain_of:
    - Biosample
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  phenotypicFeatures:
    name: phenotypicFeatures
    annotations:
      rank:
        tag: rank
        value: 7
    description: Phenotypic characteristics of the BioSample, for example histological
      findings of a biopsy.
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    multivalued: true
    alias: phenotypicFeatures
    owner: Biosample
    domain_of:
    - Phenopacket
    - Biosample
    range: PhenotypicFeature
    inlined: true
    inlined_as_list: true
  procedure:
    name: procedure
    annotations:
      rank:
        tag: rank
        value: 17
    description: Clinical procedure performed on the subject in order to extract the
      biosample. ARGO mapping specimen::specimen_anatomic_location - Procedure::body_site
      ARGO mapping specimen::specimen_acquisition_interval - Procedure::time_performed
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    exact_mappings:
    - ARGO:specimen.specimen_anatomic_location
    alias: procedure
    owner: Biosample
    domain_of:
    - Measurement
    - Biosample
    - MedicalAction
    range: Procedure
  sampleProcessing:
    name: sampleProcessing
    annotations:
      rank:
        tag: rank
        value: 20
    description: Field to represent how the sample was processed. ARGO mapping specimen::specimen_processing
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    exact_mappings:
    - ARGO:specimen.specimen_processing
    rank: 1000
    alias: sampleProcessing
    owner: Biosample
    domain_of:
    - Biosample
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  sampleStorage:
    name: sampleStorage
    annotations:
      rank:
        tag: rank
        value: 21
    description: Field to represent how the sample was stored ARGO mapping specimen::specimen_storage
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    exact_mappings:
    - ARGO:specimen.specimen_storage
    rank: 1000
    alias: sampleStorage
    owner: Biosample
    domain_of:
    - Biosample
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  sampleType:
    name: sampleType
    annotations:
      rank:
        tag: rank
        value: 6
    description: Recommended use of EFO term to describe the sample. e.g. Amplified
      DNA, ctDNA, Total RNA, Lung tissue, Cultured cells... ARGO mapping sample_registration::sample_type
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    exact_mappings:
    - ARGO:sample_registration.sample_type
    rank: 1000
    alias: sampleType
    owner: Biosample
    domain_of:
    - Biosample
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  sampledTissue:
    name: sampledTissue
    annotations:
      rank:
        tag: rank
        value: 5
    description: 'UBERON class describing the tissue from which the specimen was collected.
      PDX-MI mapping: ''Specimen tumor tissue'' FHIR mapping: Specimen.type ARGO mapping
      sample_registration::specimen_tissue_source'
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    exact_mappings:
    - ARGO:sample_registration.specimen_tissue_source
    rank: 1000
    alias: sampledTissue
    owner: Biosample
    domain_of:
    - Biosample
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  taxonomy:
    name: taxonomy
    annotations:
      rank:
        tag: rank
        value: 9
    description: NCBI taxonomic identifier (NCBITaxon) of the sample e.g. NCBITaxon:9606
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: taxonomy
    owner: Biosample
    domain_of:
    - Biosample
    - Individual
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  timeOfCollection:
    name: timeOfCollection
    annotations:
      rank:
        tag: rank
        value: 10
    description: An TimeElement describing either the age of the individual this biosample
      was derived from at the time of collection, or the time itself. See http://build.fhir.org/datatypes
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: timeOfCollection
    owner: Biosample
    domain_of:
    - Biosample
    range: TimeElement
    inlined: true
    inlined_as_list: true
  tumorGrade:
    name: tumorGrade
    annotations:
      rank:
        tag: rank
        value: 13
    description: Potentially a child term of NCIT:C28076 (Disease Grade Qualifier)
      or equivalent See https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: tumorGrade
    owner: Biosample
    domain_of:
    - Biosample
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  tumorProgression:
    name: tumorProgression
    annotations:
      rank:
        tag: rank
        value: 12
    description: Is the specimen tissue from the primary tumor, a metastasis or a
      recurrence? Most likely a child term of NCIT:C7062 (Neoplasm by Special Category)
      NCIT:C3677 (Benign Neoplasm) NCIT:C84509 (Primary Malignant Neoplasm) NCIT:C95606
      (Second Primary Malignant Neoplasm) NCIT:C3261 (Metastatic Neoplasm) NCIT:C4813
      (Recurrent Malignant Neoplasm)
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: tumorProgression
    owner: Biosample
    domain_of:
    - Biosample
    range: OntologyClass
    inlined: true
    inlined_as_list: true