Clinic Description Annotator for FHIR and SPARC
Project description
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
andcode system
are:
unit_system = "http://unitsofmeasure.org"
code_system = "http://loinc.org"
Project details
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