Measurement

The measurement element is used to record individual measurements. It can capture quantitative, ordinal (e.g., absent/present), or categorical measurements.

Data model

Definition of the Quantity element
Field Type Multiplicity Description
description string 0..1 free text.
assay OntologyClass 1..1 Class that describes the assay used to produce the measurement. REQUIRED.
measurement_value one of {Value | ComplexValue} 1..1 The result of the measurement. REQUIRED.
time_observed TimeElement 0..1 Time at which measurement was performed. RECOMMENDED.
procedure Procedure 0..1 Clinical procdure performed to acquire the sample used for the measurement

Examples

The following example shows measurement of platelet count. The result is abnormally low, but in general this element can be used to represent normal or abnormal measurements.

measurement:
    assay:
        id: "LOINC:26515-7"
        label: "Platelets [#/volume] in Blood"
    value:
        quantity:
            unit:
                id: "UO:0000316"
                label: "cells per microliter"
            value: 24000.0
    referenceRange:
        unit:
            id: "UO:0000316"
            label: "cells per microliter"
        low: 150000.0
        high: 450000.0
    timeObserved:
        timestamp: "2020-10-01T10:54:20.021Z"

The following example shows an ordinal measurement. The measurement is for nitrite in urine, and the result is positive (present).

measurement:
    assay:
        id: "LOINC:5802-4"
        label: "Nitrite [Presence] in Urine by Test strip"
    value:
        ontologyClass:
            id: "NCIT:C25626"
            label: "Present"
    timeObserved:
        timestamp: "2021-01-01T10:54:20.021Z"

This element represents a specific measurement. It may also be appropriate to represent the result of this test as a PhenotypicFeature using the HPO term Nitrituria. Which option to use depends on the analysis goals. The measurement object is intended to represent specific measurements, and the PhenotypicFeature is often used to represent a conclusion that is reached on the basis of the test.

Categorical measurements, in which the outcome of the measurement is represented by one of two or more options that are not ordered, are represented in an analogous fashion.

The following example presents a blood pressure measurement. The measurement of blood pressure consists of two measurements (systolic and diastolic), that are represented as a rstcomplexquantity.

measurement:
    assay:
      id: "CMO:0000003"
      label: "blood pressure measurement"
    complexValue:
      typedQuantities:
      - type:
          id: "NCIT:C25298"
          label: "Systolic Blood Pressure"
        quantity:
            unit:
              id: "NCIT:C49670"
              label: "Millimeter of Mercury"
            value: 125.0
      - type:
          id: "NCIT:C25299"
          label: "Diastolic Blood Pressure"
        quantity:
          unit:
            id: "NCIT:C49670"
            label: "Millimeter of Mercury"
          value: 75.0
    timeObserved:
      timestamp: "2021-01-01T10:54:20.021Z"

Explanations

description

Free-text description of the feature. Note this is not a acceptable place to document/describe t he phenotype - the type and onset etc… fields should be used for this purpose.

assay

An ontology class which describes the assay used to produce the measurement. For example “body temperature” (CMO:0000015) or “Platelets [#/volume] in Blood” (LOINC:26515-7) FHIR mapping: Observation.code

value

This element represents the result of the measurement. The measurement can be quantitative, such as LOINC:2472-9 (IgM [Mass/volume] in Serum or Plasma) or ordinal or categorical.

complex_value

This is intended to represent measurements that consist of a tightly coupled group of related quanitities. For instance, blood pressure represents a measurement of systolic and diastolic blood pressure.

time_observed

The time at which the measurement was made.

procedure

Clinical procedure performed on the subject in order to obtain the sample used for the measurement. Examples include blood draw and biopsy. If the procedure can be inferred from the measurement or if the details of the measurement are deemed unimportant (e.g., a blood glucose test is performed on a blood sample obtained with some procedure that is not specified), this element can be omitted.