Specimen

class fhir_biobank.specimen.SpecimenResource(specimen_id: str, identifier: str, specimen_material_code: str, subject: fhir_biobank.patient.PatientResource, collected_date: datetime.date, quantity: float, body_site_collection_code: Optional[str] = None, quantity_unit: Optional[str] = None, quantity_unit_code: Optional[str] = None, extensions: Optional[List[Union[fhir_biobank.diagnosis.Diagnosis, fhir_biobank.custodian.Custodian, fhir_biobank.storageTemperature.StorageTemperature]]] = None, identifier_type: str = 'ACSN')[source]

Bases: object

This class represents all the necessary information needed for a sample to be used for analysis.

Parameters

  • specimen_id (string) – Internal id that represents unique specimen, and is used for references to other resources

  • identifier (string) – used to uniquely identify specimen inside the transactions between biobanks.

  • specimen_material_code (string) – Type of material that forms the specimen. Correct values are: “whole-blood”, “bone-marrow”, “buffy-coat”, “dried-whole-blood”, “peripheral-blood-cells-vital”, “blood-plasma”, “plasma-edta”, “plasma-citrat”, “plasma-heparin”, “plasma-cell-free”, “plasma-other”, “blood-serum”, “ascites”, “csf-liquor”, “saliva”, “stool-faeces”,”urine”, “swab”, “liquid-other”, “tissue-ffpe”, “tumor-tissue-ffpe”, “normal-tissue-ffpe”, “other-tissue-ffpe”, “tissue-frozen”, “tumor-tissue-frozen”, “normal-tissue-frozen”, “other-tissue-frozen”, “tissue-other”, “dna”, “cf-dna”, “g-dna”, “rna”, “derivative-other”

  • subject (PatientResource) – class “PatientResource” representing patient from which the specimen was taken.

  • body_site_collection_code (string) – Code of the location that the specimen was collected from. Code comes from SNOMED CT

  • collected_date (date) – Time when specimen was collected from patient.

  • quantity (float) – quantity of specimen.

  • quantity_unit (string) – Unit of measure for quantity.

  • quantity_unit_code (string) – UCUM code of the quantity unit

  • extensions (List[Union[Diagnosis, Custodian, StorageTemperature]]) – List of extensions that provide addition information about the specimen. For example StorageTemperature provides additional info about how the specimen is stored

  • identifier_type (Optional[string]) – a coded type for the identifier that can be used to determine specific purpose of the identifier. default value is “ACSN” correct values are : “DL”, “PPN”, “BRN”, “MR”, “MCN”, “EN”, “TAX”, “NIIP”,”PRN”, “MD”, “DR”, “ACSN”, “UDI”, “SNO”, “SB”, “PLAC”, “FILL”, “JHN”. For more info see https://simplifier.net/packages/hl7.fhir.r4.core/4.0.1/files/82653

Raises

  • TypeError – This exception is raised when incorrect types of arguments are provided

  • ValueError – This exception is raised when incorrect value in argument is provided

property FHIRInterpretation

Getter for a FHIR object that is created from this class.

Returns

Specimen in a correct FHIR interpretation

property bodySiteCollectionCode

Getter for a body site collection code - code that defines from which part of the body the specimen was taken from.

Returns

Code of the body site

property collectedDateTime

Getter for a collected date. Indicates date which the specimen was taken.

Returns

date of the specimen collection

property extensions

Getter for list of extensions - additional information about the specimen.

Returns

List of extensions.

property identifier

Getter for identifier of the specimen.

Returns

Identifier of the specimen

property identifierType

Getter for a type of the indentifier that identifies the specimen.

Returns

code for the type of identifier

property quantity

Getter for a quantity of the specimen.

Returns

quantity of the specimen

property quantityUnit

Getter for a unit that the quantity is measured with.

Returns

unit that the quantity is measured with

property quantityUnitCode

Getter for a code that defines the quantityUnit.

Returns

code of the unit that the quantity is measured with

property specimenId

Getter for a internal id that represents unique Specimen.

Returns

str internal id used for references to other resources

specimenJSON()[source]

Method that creates JSON representation of a Specimen Resource.

Returns

FHIR Specimen resource represented in a json format.

property specimenMaterialCode

Getter for specimen material code - code that defines type of material which forms specimen.

Returns

Code of the material

property subject

Getter for a subject - PatientResource that the specimen comes from.

Returns

PatientResource indicating patient from which the specimen comes from