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: crdch:Specimen

Parents

• is_a: Entity - Any resource that has its own identifier

Referenced by class

• Diagnosis ➞related_specimen _0..* Specimen
• Specimen ➞parent_specimen _0..* Specimen

Attributes

Own

• id _0..1
  • 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.
  • Range: CrdchString
• identifier _0..*
  • 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.
  • Range: Identifier
• description _0..1
  • Description: A free text field to capture additional information or explanation about the specimen.
  • Range: CrdchString
• specimen_type _0..1
  • 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).
  • Range: CodeableConcept
  • Examples: Fresh Specimen, Portion, Aliquot, Analyte, Slide
• analyte_type _0..1
  • 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)
  • Range: CodeableConcept
  • Examples: DNA, FFPE DNA, GenomePlex (Rubicon) Amplified DNA, Repli-G (Qiagen) DNA, RNA, FFPE RNA
• associated_project _0..1
  • Description: The Project associated with the specimen.
  • Range: ResearchProject
• data_provider _0..1
  • Description: The organization (e.g.a laboratory, processing center, or research site) that provided data associated with a specimen.
  • Range: Organization
• source_material_type _0..1
  • Description: The general kind of material from which the specimen was derived.
  • Range: CodeableConcept
  • Examples: Tissue, Blood, Tumor Aspirate, Cell Line, Expanded Next Generation Cancer Model, Pleural Effusion, Xenograft Tissue
• parent_specimen _0..*
  • Description: An existing specimen from which the specimen of interest was directly derived (i.e its immediate parent specimen).
  • Range: Specimen
• source_subject _0..1
  • Description: A specific Subject from which the specimen was directly or indirectly derived.
  • Range: Subject
• tumor_status_at_collection _0..1
  • Description: The status of the tumor at the time the specimen was collected (e.g. if it was primary, recurrent, metastatic, etc).
  • Range: CodeableConcept
  • Examples: Additional Primary, Local recurrence, Metastatic, NOS, Premalignant, Primary, Recurrent, Xenograft
• creation_activity _0..1
  • Description: The activity through which a specimen was created, by removing material from an biological subject, or deriving material from an existing specimen.
  • Range: SpecimenCreationActivity
• processing_activity _0..*
  • Description: An activity that modifies the physical structure, composition, or state of a specimen.
  • Range: SpecimenProcessingActivity
• storage_activity _0..*
  • Description: An activity that results in the storage or maintenance of a specimen in a particular location, container, or state.
  • Range: SpecimenStorageActivity
• transport_activity _0..*
  • Description: An activity through which the specimen is transported between locations.
  • Range: SpecimenTransportActivity
• contained_in _0..1
  • 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)
  • Range: SpecimenContainer
• dimensional_measures _0..1
  • Description: Observations about the current physical dimensions of an object (e.g. length, width, area).
  • Range: DimensionalObservationSet
• quantity_measure _0..*
  • Description: An observation related to the present quantity of a specimen - e.g. its weight, volume, or analyte concentration.
  • Range: SpecimenQuantityObservation
• quality_measure _0..*
  • Description: An observation about characteristics of a specimen that are indicative of its quality or suitability for use.
  • Range: SpecimenQualityObservation
• cellular_composition_type _0..1
  • Description: A term describing the type of cell or cellular material comprising a specimen.
  • Range: CodeableConcept
  • Examples: 2D Classical Conditionally Reprogrammed Cells, Adherent Cell Line, Bone Marrow Components, Buccal Cells, Buffy Coat, Derived Cell Line, Granulocytes, Pleural Effusion, Human Original Cells, Liquid Suspension Cell Line
• histological_composition_measures _0..*
  • Description: A set of one or more observations that quantify the relative or absolute composition of a specimen at cellular level - e.g. how many cells in the specimen are of a given type, or exhibit a particular cellular phenotype.
  • Range: HistologicalCompositionObservationSet
• general_tissue_pathology _0..1
  • Description: The high-level kind of tissue collected when generating a specimen, based on its disease status or proximity to tumor tissue (e.g. is it normal, abnormal, tumor, tumor-adjacent).
  • Range: CodeableConcept
  • Examples: Tumor, Normal, Abnormal, Peritumoral, not applicable
• specific_tissue_pathology _0..1
  • Description: A term describing the specific pathology exhibited by the tissue comprising a specimen.
  • Range: CodeableConcept
  • Examples: Non cancerous tissue, Lung Cancer (all types), CNS, medulloblastoma, 00, 01, 02, Melanocytic hyperplasia, Atypical melanocytic proliferation, Melanoma in situ, superficial spreading
• preinvasive_tissue_morphology _0..1
  • Description: A term describing the specific pathology exhibited by pre-invasive tissue comprising a specimen.
  • Range: CodeableConcept
• morphology_pathologically_confirmed _0..1
  • Description: A flag indicating whether the histologic assessment of specific morphology was confirmed by pathologist review.
  • Range: CrdchBoolean
• morphology_assessor_role _0..1
  • Description: A term describing the role of the person who histologically assessed the specific tissue morphology of a specimen
  • Range: CodeableConcept
  • Examples: Pathologist, Research Scientist, Other, Unknown
• morphology_assessment_method _0..1
  • Description: The general method used to assess a specimens specific tissue morphology
  • Range: CodeableConcept
  • Examples: Digital, Microscopy, Other, Unknown
• degree_of_dysplasia _0..1
  • Description: A term describing the nature/extent of abnormal cells that are not cancer, as observed upon microscopic assessment of a specimen. Records the degree of dysplasia for the cyst or lesion under consideration.
  • Range: CodeableConcept
  • Examples: Normal or basal cell hyperplasia or metaplasia, Mild dysplasia, Moderate dysplasia, Severe dysplasia, Carcinoma in Situ, Unknown
• dysplasia_fraction _0..1
  • Description: Resulting value to represent the number of pieces of dysplasia divided by the total number of pieces.
  • Range: CrdchString
• related_document _0..*
  • 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)
  • Range: Document
• section_location _0..1
  • Description: The location in a parent specimen from which a section/portion was excised (e.g. top, middle, bottom)
  • Range: CodeableConcept
  • Examples: Top, Bottom, Unknown
• derived_product _0..*
  • Description: A 'living' biologically active product that was derived from the specimen (e.g. a cell culture, tissue culture, or organoid)
  • Range: BiologicProduct
• distance_from_paired_specimen _0..1
  • Description: The observed distance in the body of the specimen from a 'paired specimen' at the time of collection. (e.g. the distance between the in vivo location of a tumor tissue specimen and its paired normal specimen)
  • Range: Quantity

Other properties

Comments:		Definition adapted from FHIR Specimen.