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: ccdh:Specimen

Parents

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

Referenced by class

• None ➞derived_from_specimen _0..* Specimen

Attributes

Own

• Specimen➞id _REQ
  • Description: The ‘logical’ identifier of the entity in the system of record, e.g. a UUID. This ‘id’ is unique within a given system. The identified entity may have a different ‘id’ in a different system.
  • range: String
• ➞analyte_concentration _OPT
  • Description: The concentration of an extracted analyte that is present in a specimen (specifically, in a specimen of type ‘analyte’, or an ‘aliquot’ derived from an analyte). e.g. the concentration of DNA in a specimen created through extracting DNA from a blood sample.
  • range: Quantity
• ➞analyte_concentration_method _OPT
  • Description: The method used to determine the concentration of purified analyte within a solution.
  • range: CodeableConcept
• ➞analyte_type _OPT
  • Description: When the specimen is of type ‘analyte’ or ‘aliquot’, this is the type of substance the analyte represents (e.g. DNA, RNA)
  • range: CodeableConcept
• ➞associated_project _OPT
  • Description: The Project associated with the specimen.
  • range: Project
• ➞cellular_composition _OPT
  • Description: The cellular composition of the sample
  • range: CodeableConcept
• ➞current_volume _0..*
  • Description: The current total volume of the specimen, at the time of recording.
  • range: Quantity
• ➞current_weight _0..*
  • Description: The current weight of the specimen, at the time of recording (as opposed to an initial weight before its processing or portioning).
  • range: Quantity
• ➞derived_from_specimen _0..*
  • Description: A source/parent specimen from which this one was directly derived.
  • range: Specimen
• ➞derived_from_subject _OPT
  • Description: The Patient/ResearchSubject, or Biologically Derived Materal (e.g. a cell line, tissue culture, organoid) from which the specimen was directly or indirectly derived.
  • range: Patient
• ➞general_tissue_morphology _OPT

  • Description: A term describing at a high-level the kind of tissue collected in a specimen, with respect to disease status or proximity to tumor tissue (e.g. is it normal, abnormal, tumor, tumor-adjacent).

  • range: CodeableConcept

• ➞identifier _0..*
  • Description: A ‘business’ identifier or accession number for the entity, typically as provided by an external system or authority, that persists across implementing systems (i.e. a ‘logical’ identifier).
  • range: Identifier
• ➞matched_normal_flag _0..*
  • Description: A flag indicating that there is no matched normal aliquot for this case that can be used for variant calling purposes.
  • range: CodeableConcept
• ➞qualification_status_flag _OPT
  • Description: A flag indicating whether the specimen is qualified or disqualified for data analysis in a study.
  • range: CodeableConcept
• ➞source_material_type _OPT
  • Description: The general kind of material from which the specimen was derived, indicating the physical nature of the source material.
  • range: CodeableConcept
• ➞specific_tissue_morphology _OPT
  • Description: A term describing the specific pathology exhibited by the tissue in a specimen.
  • range: CodeableConcept
• ➞specimen_type _OPT

  • Description: The high-level type of the specimen, based on its how it has been derived from the original extracted sample.

  • range: CodeableConcept