fhir-cda 1.0.6

Clinic Description Annotator for FHIR and SPARC

Clinical Description Annotator

Annotator for annotating measurement results, workflows, workflow tools, models, and workflow tool process datasets in SPARC SDS datasets to the data format required for digitaltwins-on-fhir.

Usage

Annotator measurements for SPARC SDS dataset

• Add measurement for one patient

from fhir_cda import Annotator
from fhir_cda.ehr import Measurement, ObservationValue, Quantity

annotator = Annotator("./dataset/dataset-sparc").measurements()

m = Measurement(
    value=ObservationValue(
        value_quantity=Quantity(
            value=30,
            unit="year",
            code="a")),
    code="30525-0")

annotator.add_measurements("sub-001", m).save()

• Add measurements for one patient

m1 = Measurement(
    value=ObservationValue(
        value_quantity=Quantity(
            value=0.15,
            unit="cm",
            code="cm")),
    code="21889-1")
m2 = Measurement(
    value=ObservationValue(
        value_quantity=Quantity(
            value=0.15,
            unit="cm",
            code="cm",
            system="http://unitsofmeasure.org")),
    code="21889-1",
    code_system="http://loinc.org",
    display="Size Tumor")
annotator.add_measurements("sub-001", [m1, m2]).save()

• Add measurement for multiple patients

m = Measurement(
    value=ObservationValue(value_string="Female"),
    code="99502-7",
    display="Recorded sex or gender",
    code_system="http://loinc.org")
annotator.add_measurements(["sub-001", "sub-002"], m).save()

• A measurements for multiple patients

m1 = Measurement(
    value=ObservationValue(value_string="Female"),
    code="99502-7",
    display="Recorded sex or gender",
    code_system="http://loinc.org")
m2 = Measurement(
    value=ObservationValue(
        value_quantity=Quantity(
            value=0.15,
            unit="cm",
            code="cm",
            system="http://unitsofmeasure.org")),
    code="21889-1",
    code_system="http://loinc.org",
    display="Size Tumor")
annotator.add_measurements(["sub-001", "sub-002"], [m1, m2])
annotator.save()

• Notice: The default value for unit system and code system are:

unit_system = "http://unitsofmeasure.org"
code_system = "http://loinc.org"