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"