Class: Specimen

Any material taken as a sample from a biological entity (living or dead), or from a physical object or the environment. Specimens are usually collected as an example of their kind, often for use in some investigation.

URI: bdchm:Specimen

classDiagram class Specimen Entity <|-- Specimen Specimen : analyte_type Specimen --> AnalyteTypeEnum : analyte_type Specimen : cellular_composition_type Specimen : contained_in Specimen --> SpecimenContainer : contained_in Specimen : creation_activity Specimen --> SpecimenCreationActivity : creation_activity Specimen : derived_product Specimen --> BiologicProduct : derived_product Specimen : description Specimen : dimensional_measures Specimen --> DimensionalObservationSet : dimensional_measures Specimen : id Specimen : identity Specimen --> Identifier : identity Specimen : parent_specimen Specimen --> Specimen : parent_specimen Specimen : processing_activity Specimen --> SpecimenProcessingActivity : processing_activity Specimen : quality_measure Specimen --> SpecimenQualityObservation : quality_measure Specimen : quantity_measure Specimen --> SpecimenQuantityObservation : quantity_measure Specimen : related_document Specimen --> Document : related_document Specimen : section_location Specimen --> SectionLocationEnum : section_location Specimen : source_material_type Specimen --> SourceMaterialTypeEnum : source_material_type Specimen : source_participant Specimen --> Participant : source_participant Specimen : specimen_type Specimen --> SpecimenTypeEnum : specimen_type Specimen : storage_activity Specimen --> SpecimenStorageActivity : storage_activity Specimen : transport_activity Specimen --> SpecimenTransportActivity : transport_activity

Inheritance

Entity
- Specimen

Slots

Name	Cardinality and Range	Description	Inheritance
identity	0..* Identifier	A 'business' identifier or accession number for the entity, typically as prov...	direct
description	0..1 String	A free text field to capture additional information or explanation about the ...	direct
specimen_type	0..1 SpecimenTypeEnum	The high-level type of the specimen, based on its derivation provenance (i	direct
analyte_type	0..1 AnalyteTypeEnum	For specimens of type 'analyte' (or an 'aliquot' derived from an analyte), th...	direct
source_material_type	0..1 SourceMaterialTypeEnum	The general kind of material from which the specimen was derived	direct
parent_specimen	0..* Specimen	An existing specimen from which the specimen of interest was directly derived...	direct
source_participant	0..1 Participant	A specific Subject from which the specimen was directly or indirectly derived	direct
creation_activity	0..1 SpecimenCreationActivity	The activity through which a specimen was created, by removing material from ...	direct
processing_activity	0..* SpecimenProcessingActivity	An activity that modifies the physical structure, composition, or state of a ...	direct
storage_activity	0..* SpecimenStorageActivity	An activity that results in the storage or maintenance of a specimen in a par...	direct
transport_activity	0..* SpecimenTransportActivity	An activity through which the specimen is transported between locations	direct
contained_in	0..1 SpecimenContainer	A physical container in which a specimen is presently held or attached - as ...	direct
dimensional_measures	0..1 DimensionalObservationSet	Observations about the current physical dimensions of an object (e	direct
quantity_measure	0..* SpecimenQuantityObservation	An observation related to the present quantity of a specimen - e	direct
quality_measure	0..* SpecimenQualityObservation	An observation about characteristics of a specimen that are indicative of its...	direct
cellular_composition_type	0..1 String	A term describing the type of cell or cellular material comprising a specimen	direct
related_document	0..* Document	A reference to an external document that is about or related to the specimen ...	direct
section_location	0..1 SectionLocationEnum	The location in a parent specimen from which a section/portion was excised (e	direct
derived_product	0..* BiologicProduct	A 'living' biologically active product that was derived from the specimen (e	direct
id	1..1 Uriorcurie	The 'logical' identifier of the entity within the system of record	Entity

Usages

used by	used in	type	used
Specimen	parent_specimen	range	Specimen
SpecimenQualityObservation	focus	range	Specimen
SpecimenQuantityObservation	focus	range	Specimen

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/nhlbidatastage/bdchm

Mappings

Mapping Type	Mapped Value
self	bdchm:Specimen
native	bdchm:Specimen

LinkML Source

Direct

name: Specimen
description: Any material taken as a sample from a biological entity (living or dead),
  or from a physical object or the environment. Specimens are usually collected as
  an example of their kind, often for use in some investigation.
from_schema: https://w3id.org/nhlbidatastage/bdchm
is_a: Entity
slots:
- identity
attributes:
  description:
    name: description
    description: A free text field to capture additional information or explanation
      about the specimen.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    multivalued: false
    range: string
    required: false
  specimen_type:
    name: specimen_type
    description: The high-level type of the specimen, based on its derivation provenance
      (i.e. how far removed it is from the original sample extracted from a source).
    examples:
    - value: Fresh Specimen
    - value: Portion
    - value: Aliquot
    - value: Analyte
    - value: Slide
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    values_from:
    - crdch:enum_CRDCH_Specimen_specimen_type
    multivalued: false
    range: SpecimenTypeEnum
    required: false
  analyte_type:
    name: analyte_type
    description: For specimens of type 'analyte' (or an 'aliquot' derived from an
      analyte), this is the category of chemcial the analyte of interest represents
      (e.g. DNA, RNA)
    examples:
    - value: DNA
    - value: FFPE DNA
    - value: GenomePlex (Rubicon) Amplified DNA
    - value: Repli-G (Qiagen) DNA
    - value: RNA
    - value: FFPE RNA
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    values_from:
    - crdch:enum_CRDCH_Specimen_analyte_type
    multivalued: false
    range: AnalyteTypeEnum
    required: false
  source_material_type:
    name: source_material_type
    description: The general kind of material from which the specimen was derived.
    comments:
    - Values captured here may describe the type of molecular mixture, cell, tissue,
      organ, body fluid, embryo, excretory substance, or experimental system from
      which a specimen was derived.
    examples:
    - value: Tissue
    - value: Blood
    - value: Tumor Aspirate
    - value: Cell Line
    - value: Expanded Next Generation Cancer Model
    - value: Pleural Effusion
    - value: Xenograft Tissue
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: false
    range: SourceMaterialTypeEnum
    required: false
  parent_specimen:
    name: parent_specimen
    description: An existing specimen from which the specimen of interest was directly
      derived (i.e its immediate parent specimen).
    comments:
    - This property indicates only the direct parent specimen(s).  Cardinality is
      0..m to account for specimens derived from pooling of multiple specimens.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: true
    range: Specimen
    required: false
    inlined: true
    inlined_as_list: true
  source_participant:
    name: source_participant
    description: A specific Subject from which the specimen was directly or indirectly
      derived.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: false
    range: Participant
    required: false
  creation_activity:
    name: creation_activity
    description: The activity through which a specimen was created, by removing material
      from an biological subject, or deriving material from an existing specimen.
    comments:
    - Note that a given specimen is the result of only one and only one SpecimenCreationActivity,
      but may be subject to many processing events that subsequently modify or derive
      new specimens from it.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: false
    range: SpecimenCreationActivity
    required: false
  processing_activity:
    name: processing_activity
    description: An activity that modifies the physical structure, composition, or
      state of a specimen.
    comments:
    - Note that a given specimen may undergo more than one distinct processing activity,
      through application of different methodologies that modify its physical state.
      However, if an activity generates a new specimen (e.g. via portioning, slicing)
      it is considered a SpeciemnCreationActivity.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: true
    range: SpecimenProcessingActivity
    required: false
  storage_activity:
    name: storage_activity
    description: An activity that results in the storage or maintenance of a specimen
      in a particular location, container, or state.
    comments:
    - 'The 0..m cardinality of this attribute reflects the fact that a given specimen
      may undergo many separate periods of storage, in different locations and/or
      under different conditions '
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: true
    range: SpecimenStorageActivity
    required: false
  transport_activity:
    name: transport_activity
    description: An activity through which the specimen is transported between locations.
    comments:
    - The 0..m cardinality of this attribute reflects the fact that a given specimen
      may undergo many separate transport processes at different periods of time.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: true
    range: SpecimenTransportActivity
    required: false
  contained_in:
    name: contained_in
    description: A physical container in which a specimen is presently held or attached
      -  as storage for future use,  a substrate for growth (e.g. a cell culture dish),
      or a vessel to enable analysis (e.g. a microscope slide or 96-well plate)
    comments:
    - 'The 0..1 cardinality on this attribute means that you cannot directly references
      multiple nested containers holding a sample. To capture this scenario, use the
      ''parent_container'' attribute of the Container entity.  '
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: false
    range: SpecimenContainer
    required: false
  dimensional_measures:
    name: dimensional_measures
    description: Observations about the current physical dimensions of an object (e.g.
      length, width, area).
    comments:
    - Observations are flexible containers for capturing a specific type of observation/measurement
      data about an object, along with metadata about how it was generated. The specific
      type of observation made is captured as data in the Observation object.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: false
    range: DimensionalObservationSet
    required: false
  quantity_measure:
    name: quantity_measure
    description: An observation related to the present quantity of a specimen - e.g.
      its weight, volume, or analyte concentration.
    comments:
    - Observations are flexible containers for capturing a specific type of observation/measurement
      data about an object, along with metadata about how it was generated. The specific
      type of observation made is captured as data in the Observation object.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: true
    range: SpecimenQuantityObservation
    required: false
  quality_measure:
    name: quality_measure
    description: An observation about characteristics of a specimen that are indicative
      of its quality or suitability for use.
    comments:
    - Observations are flexible containers for capturing a specific type of observation/measurement
      data about an object, along with metadata about how it was generated. The specific
      type of observation made is captured as data in the Observation object.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: true
    range: SpecimenQualityObservation
    required: false
  cellular_composition_type:
    name: cellular_composition_type
    description: A term describing the type of cell or cellular material comprising
      a specimen.
    examples:
    - value: 2D Classical Conditionally Reprogrammed Cells
    - value: Adherent Cell Line
    - value: Bone Marrow Components
    - value: Buccal Cells
    - value: Buffy Coat
    - value: Derived Cell Line
    - value: Granulocytes
    - value: Pleural Effusion
    - value: Human Original Cells
    - value: Liquid Suspension Cell Line
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    values_from:
    - crdch:enum_CRDCH_Specimen_cellular_composition_type
    multivalued: false
    range: string
    required: false
  related_document:
    name: related_document
    description: A reference to an external document that is about or related to the
      specimen (e.g. a publication related to the study it is a part of, pathology
      report containing additional details about it, protocol describing how it was
      collected)
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: true
    range: Document
    required: false
  section_location:
    name: section_location
    description: The location in a parent specimen from which a section/portion was
      excised (e.g. top, middle, bottom)
    comments:
    - This attribute applies only to Specimens that are of type 'portion' or 'slide'.
    examples:
    - value: Top
    - value: Bottom
    - value: Unknown
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    values_from:
    - crdch:enum_CRDCH_Specimen_section_location
    multivalued: false
    range: SectionLocationEnum
    required: false
  derived_product:
    name: derived_product
    description: A 'living' biologically active product that was derived from the
      specimen (e.g. a cell culture, tissue culture, or organoid)
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: true
    range: BiologicProduct
    required: false
    inlined: true
    inlined_as_list: true

Induced

name: Specimen
description: Any material taken as a sample from a biological entity (living or dead),
  or from a physical object or the environment. Specimens are usually collected as
  an example of their kind, often for use in some investigation.
from_schema: https://w3id.org/nhlbidatastage/bdchm
is_a: Entity
attributes:
  description:
    name: description
    description: A free text field to capture additional information or explanation
      about the specimen.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    multivalued: false
    alias: description
    owner: Specimen
    domain_of:
    - Participant
    - ResearchStudy
    - Questionnaire
    - Document
    - Specimen
    - BiologicProduct
    range: string
    required: false
  specimen_type:
    name: specimen_type
    description: The high-level type of the specimen, based on its derivation provenance
      (i.e. how far removed it is from the original sample extracted from a source).
    examples:
    - value: Fresh Specimen
    - value: Portion
    - value: Aliquot
    - value: Analyte
    - value: Slide
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    values_from:
    - crdch:enum_CRDCH_Specimen_specimen_type
    multivalued: false
    alias: specimen_type
    owner: Specimen
    domain_of:
    - Specimen
    range: SpecimenTypeEnum
    required: false
  analyte_type:
    name: analyte_type
    description: For specimens of type 'analyte' (or an 'aliquot' derived from an
      analyte), this is the category of chemcial the analyte of interest represents
      (e.g. DNA, RNA)
    examples:
    - value: DNA
    - value: FFPE DNA
    - value: GenomePlex (Rubicon) Amplified DNA
    - value: Repli-G (Qiagen) DNA
    - value: RNA
    - value: FFPE RNA
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    values_from:
    - crdch:enum_CRDCH_Specimen_analyte_type
    multivalued: false
    alias: analyte_type
    owner: Specimen
    domain_of:
    - Specimen
    range: AnalyteTypeEnum
    required: false
  source_material_type:
    name: source_material_type
    description: The general kind of material from which the specimen was derived.
    comments:
    - Values captured here may describe the type of molecular mixture, cell, tissue,
      organ, body fluid, embryo, excretory substance, or experimental system from
      which a specimen was derived.
    examples:
    - value: Tissue
    - value: Blood
    - value: Tumor Aspirate
    - value: Cell Line
    - value: Expanded Next Generation Cancer Model
    - value: Pleural Effusion
    - value: Xenograft Tissue
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: false
    alias: source_material_type
    owner: Specimen
    domain_of:
    - Specimen
    range: SourceMaterialTypeEnum
    required: false
  parent_specimen:
    name: parent_specimen
    description: An existing specimen from which the specimen of interest was directly
      derived (i.e its immediate parent specimen).
    comments:
    - This property indicates only the direct parent specimen(s).  Cardinality is
      0..m to account for specimens derived from pooling of multiple specimens.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: true
    alias: parent_specimen
    owner: Specimen
    domain_of:
    - Specimen
    range: Specimen
    required: false
    inlined: true
    inlined_as_list: true
  source_participant:
    name: source_participant
    description: A specific Subject from which the specimen was directly or indirectly
      derived.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: false
    alias: source_participant
    owner: Specimen
    domain_of:
    - Specimen
    range: Participant
    required: false
  creation_activity:
    name: creation_activity
    description: The activity through which a specimen was created, by removing material
      from an biological subject, or deriving material from an existing specimen.
    comments:
    - Note that a given specimen is the result of only one and only one SpecimenCreationActivity,
      but may be subject to many processing events that subsequently modify or derive
      new specimens from it.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: false
    alias: creation_activity
    owner: Specimen
    domain_of:
    - Specimen
    range: SpecimenCreationActivity
    required: false
  processing_activity:
    name: processing_activity
    description: An activity that modifies the physical structure, composition, or
      state of a specimen.
    comments:
    - Note that a given specimen may undergo more than one distinct processing activity,
      through application of different methodologies that modify its physical state.
      However, if an activity generates a new specimen (e.g. via portioning, slicing)
      it is considered a SpeciemnCreationActivity.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: true
    alias: processing_activity
    owner: Specimen
    domain_of:
    - Specimen
    range: SpecimenProcessingActivity
    required: false
  storage_activity:
    name: storage_activity
    description: An activity that results in the storage or maintenance of a specimen
      in a particular location, container, or state.
    comments:
    - 'The 0..m cardinality of this attribute reflects the fact that a given specimen
      may undergo many separate periods of storage, in different locations and/or
      under different conditions '
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: true
    alias: storage_activity
    owner: Specimen
    domain_of:
    - Specimen
    range: SpecimenStorageActivity
    required: false
  transport_activity:
    name: transport_activity
    description: An activity through which the specimen is transported between locations.
    comments:
    - The 0..m cardinality of this attribute reflects the fact that a given specimen
      may undergo many separate transport processes at different periods of time.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: true
    alias: transport_activity
    owner: Specimen
    domain_of:
    - Specimen
    range: SpecimenTransportActivity
    required: false
  contained_in:
    name: contained_in
    description: A physical container in which a specimen is presently held or attached
      -  as storage for future use,  a substrate for growth (e.g. a cell culture dish),
      or a vessel to enable analysis (e.g. a microscope slide or 96-well plate)
    comments:
    - 'The 0..1 cardinality on this attribute means that you cannot directly references
      multiple nested containers holding a sample. To capture this scenario, use the
      ''parent_container'' attribute of the Container entity.  '
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: false
    alias: contained_in
    owner: Specimen
    domain_of:
    - Specimen
    range: SpecimenContainer
    required: false
  dimensional_measures:
    name: dimensional_measures
    description: Observations about the current physical dimensions of an object (e.g.
      length, width, area).
    comments:
    - Observations are flexible containers for capturing a specific type of observation/measurement
      data about an object, along with metadata about how it was generated. The specific
      type of observation made is captured as data in the Observation object.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: false
    alias: dimensional_measures
    owner: Specimen
    domain_of:
    - Specimen
    range: DimensionalObservationSet
    required: false
  quantity_measure:
    name: quantity_measure
    description: An observation related to the present quantity of a specimen - e.g.
      its weight, volume, or analyte concentration.
    comments:
    - Observations are flexible containers for capturing a specific type of observation/measurement
      data about an object, along with metadata about how it was generated. The specific
      type of observation made is captured as data in the Observation object.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: true
    alias: quantity_measure
    owner: Specimen
    domain_of:
    - Specimen
    range: SpecimenQuantityObservation
    required: false
  quality_measure:
    name: quality_measure
    description: An observation about characteristics of a specimen that are indicative
      of its quality or suitability for use.
    comments:
    - Observations are flexible containers for capturing a specific type of observation/measurement
      data about an object, along with metadata about how it was generated. The specific
      type of observation made is captured as data in the Observation object.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: true
    alias: quality_measure
    owner: Specimen
    domain_of:
    - Specimen
    range: SpecimenQualityObservation
    required: false
  cellular_composition_type:
    name: cellular_composition_type
    description: A term describing the type of cell or cellular material comprising
      a specimen.
    examples:
    - value: 2D Classical Conditionally Reprogrammed Cells
    - value: Adherent Cell Line
    - value: Bone Marrow Components
    - value: Buccal Cells
    - value: Buffy Coat
    - value: Derived Cell Line
    - value: Granulocytes
    - value: Pleural Effusion
    - value: Human Original Cells
    - value: Liquid Suspension Cell Line
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    values_from:
    - crdch:enum_CRDCH_Specimen_cellular_composition_type
    multivalued: false
    alias: cellular_composition_type
    owner: Specimen
    domain_of:
    - Specimen
    range: string
    required: false
  related_document:
    name: related_document
    description: A reference to an external document that is about or related to the
      specimen (e.g. a publication related to the study it is a part of, pathology
      report containing additional details about it, protocol describing how it was
      collected)
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: true
    alias: related_document
    owner: Specimen
    domain_of:
    - Specimen
    range: Document
    required: false
  section_location:
    name: section_location
    description: The location in a parent specimen from which a section/portion was
      excised (e.g. top, middle, bottom)
    comments:
    - This attribute applies only to Specimens that are of type 'portion' or 'slide'.
    examples:
    - value: Top
    - value: Bottom
    - value: Unknown
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    values_from:
    - crdch:enum_CRDCH_Specimen_section_location
    multivalued: false
    alias: section_location
    owner: Specimen
    domain_of:
    - Specimen
    range: SectionLocationEnum
    required: false
  derived_product:
    name: derived_product
    description: A 'living' biologically active product that was derived from the
      specimen (e.g. a cell culture, tissue culture, or organoid)
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: true
    alias: derived_product
    owner: Specimen
    domain_of:
    - Specimen
    range: BiologicProduct
    required: false
    inlined: true
    inlined_as_list: true
  identity:
    name: identity
    description: A 'business' identifier or accession number for the entity, typically
      as provided by an external system or authority, that are globally unique and
      persist across implementing systems. Also, since these identifiers are created
      outside the information system through a specific business process, the Identifier
      type has additional attributes to capture this additional metadata so the actual
      identifier values are qualified by the context that created those values. This
      additional context allows "identifier" instances to be transmitted as business
      data across systems while still being able to trace them back to the system
      of origin.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    slot_uri: schema:identifier
    multivalued: true
    alias: identity
    owner: Specimen
    domain_of:
    - Person
    - Demography
    - Participant
    - ResearchStudy
    - Organization
    - Questionnaire
    - QuestionnaireItem
    - Condition
    - Document
    - Specimen
    - BiologicProduct
    range: Identifier
  id:
    name: id
    description: The 'logical' identifier of the entity within the system of record.  The
      simple value of this attribute stands for an identifier of this data object
      within the system, it can be used as a reference from other objects within the
      same system (i.e. primary and foreign keys), and it should be unique per type
      of object. The same data object copied to a different system will likely have
      a different "id" in the new system since "id" values are system specific and
      do not represent persistent business identifiers. Business identifiers are assigned
      outside the information system and are captured in the "identifier" field. The
      "id" field is more likely to be a serially or randomly generated value that
      is assigned to the data object as it is created in a system.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    slot_uri: schema:identifier
    identifier: true
    alias: id
    owner: Specimen
    domain_of:
    - Entity
    range: uriorcurie
    required: true