A complete example: COVID-19

Here, we demonstrate how phenopackets are used to represent the time course of a case of severe COVID-19 based on a published case report. We will explain each of the components of the phenopacket in order.

subject

The subject is a 70 year-old male who died owing to complications of COVID-19. The time and cause of death are represented by the VitalStatus element. Note that the timestamp is with reference to the Unix time, defined as the number of seconds that have elapsed since the Unix epoch, minus leap seconds; the Unix epoch is 00:00:00 UTC on 1 January 1970. Thus, 1585353600 corresponds to Saturday March 28, 2020 00:00:00 (AM).

subject:
   id: "P123542"
   sex: "MALE"
   timeAtLastEncounter:
     age:
       iso8601duration: "P70Y"
   vitalStatus:
     status: "DECEASED"
     timeOfDeath:
       timestamp: "2020-03-28T00:00:00Z"
     causeOfDeath:
       id: "MONDO:0100096"
       label: "COVID-19"

phenotypicFeatures

The phenotypic features here describe the more qualitative phenotypic features the patient exhibited. He is described as having an A+ blood group and suffering from a fever, flank pain, hematuria and later on myalgia, diarrhea and dyspnea which develops into acute respiratory failure three days after the initial onset of symptoms at which point he is admitted into hospital.

phenotypicFeatures:
- type:
    id: "NCIT:C76246"
    label: "Blood Group A"
- type:
    id: "NCIT:C76251"
    label: "Rh Positive Blood Group"
- type:
    id: "NCIT:C3038"
    label: "Fever"
  onset:
    timestamp: "2020-03-17T00:00:00Z"
- type:
    id: "NCIT:C34615"
    label: "Flank Pain"
  onset:
    timestamp: "2020-03-17T00:00:00Z"
- type:
    id: "NCIT:C3090"
    label: "Hematuria"
  onset:
    timestamp: "2020-03-17T00:00:00Z"
- type:
    id: "NCIT:C27009"
    label: "Myalgia"
  onset:
    interval:
      start: "2020-03-18T00:00:00Z"
      end: "2020-03-20T00:00:00Z"
- type:
    id: "NCIT:C2987"
    label: "Diarrhea"
  onset:
    interval:
      start: "2020-03-18T00:00:00Z"
      end: "2020-03-20T00:00:00Z"
- type:
    id: "NCIT:C2998"
    label: "Dyspnea"
  onset:
    interval:
      start: "2020-03-18T00:00:00Z"
      end: "2020-03-20T00:00:00Z"
- type:
    id: "NCIT:C27043"
    label: "Acute Respiratory Failure"
  onset:
    timestamp: "2020-03-20T00:00:00Z"

measurements

The measurements block allows quantitative recording of measurements as opposed to qualitative. For example ‘Fever’ (NCIT:C3038) listed in the phenotypicFeatures section could be represented quantitatively as a Measurement rather than a PhenotypicFeature.

In this section we show two of the measurements for the absolute blood lymphocyte count listed in table 1 of the reference. This shows the historical count from measurements taken within the six months prior to hospital admission, followed by the count taken on admission.

measurements:
- assay:
    id: "NCIT:C113237"
    label: "Absolute Blood Lymphocyte Count"
  value:
    quantity:
      unit:
        id: "NCIT:C67245"
        label: "Thousand Cells"
      value: 1.4
      referenceRange:
        unit:
          id: "NCIT:C67245"
          label: "Thousand Cells"
        low: 1.0
        high: 4.5
  timeObserved:
    interval:
      start: "2019-09-01T00:00:00Z"
      end: "2020-03-01T00:00:00Z"
- assay:
    id: "NCIT:C113237"
    label: "Absolute Blood Lymphocyte Count"
  value:
    quantity:
      unit:
        id: "NCIT:C67245"
        label: "Thousand Cells"
      value: 0.7
      referenceRange:
        unit:
          id: "NCIT:C67245"
          label: "Thousand Cells"
        low: 1.0
        high: 4.5
  timeObserved:
    timestamp: "2020-03-20T00:00:00Z"

diseases

This section displays a selection of the patient’s prior medical history, without any timeframe indicating it included ischemic cardiomyopathy, stage 3 chronic kidney disease and obesity. He did not have diabetes. He had a positive PCR test for COVID-19 three days before admission to hospital.

diseases:
- term:
    id: "NCIT:C2985"
    label: "Diabetes Mellitus"
  excluded: true
- term:
    id: "NCIT:C34830"
    label: "Cardiomyopathy"
- term:
    id: "NCIT:C80389"
    label: "Chronic Kidney Disease, Stage 3"
- term:
    id: "NCIT:C3283"
    label: "Obesity"
- term:
    id: "MONDO:0100096"
    label: "COVID-19"
  onset:
    timestamp: "2020-03-17T00:00:00Z"

medicalActions

As post of his medical history it was noted he had previously had a left ventricular assist device implanted at some point in 2016. Given this as not precisely specified a timestamp for Jan 1st 2016 is stated. Once admitted to hospital for acute respiratory failure as a result of the COVID-19 infection the patient was administered nasal oxygen at 2L/min for two days before requiring the dosage to be increased to 50L/min on day 2. Days 2 - 8, the patient required intubation and oxygen was delivered via a positive end expiratory pressure valve device. He was treated with hydroxychloroquine for the first 2 days before being administered Tocilizumab.

medicalActions:
- procedure:
    code:
      id: "NCIT:C80473"
      label: "Left Ventricular Assist Device"
    performed:
      timestamp: "2016-01-01T00:00:00Z"
- treatment:
    agent:
      id: "NCIT:C722"
      label: "Oxygen"
    routeOfAdministration:
      id: "NCIT:C38284"
      label: "Nasal Route of Administration"
    doseIntervals:
    - quantity:
        unit:
          id: "NCIT:C67388"
          label: "Liter per Minute"
        value: 2.0
      interval:
        start: "2020-03-20T00:00:00Z"
        end: "2020-03-22T00:00:00Z"
    - quantity:
        unit:
          id: "NCIT:C67388"
          label: "Liter per Minute"
        value: 50.0
      interval:
        start: "2020-03-22T00:00:00Z"
        end: "2020-03-23T00:00:00Z"
- treatment:
    agent:
      id: "NCIT:C557"
      label: "Hydroxychloroquine"
    doseIntervals:
    - quantity:
        unit:
          id: "NCIT:C28253"
          label: "mg"
        value: 450.0
      scheduleFrequency:
        id: "NCIT:C64496"
        label: "Twice Daily"
      interval:
        start: "2020-03-20T00:00:00Z"
        end: "2020-03-20T00:00:00Z"
    - quantity:
        unit:
          id: "NCIT:C28253"
          label: "mg"
        value: 450.0
      scheduleFrequency:
        id: "NCIT:C125004"
        label: "Once Daily"
      interval:
        start: "2020-03-21T00:00:00Z"
        end: "2020-03-22T00:00:00Z"
- procedure:
    code:
      id: "NCIT:C116648"
      label: "Tracheal Intubation"
    performed:
      timestamp: "2020-03-22T00:00:00Z"
- treatment:
    agent:
      id: "NCIT:C722"
      label: "Oxygen"
    routeOfAdministration:
      id: "NCIT:C50254"
      label: "Positive end Expiratory Pressure Valve Device"
    doseIntervals:
    - quantity:
        unit:
          id: "NCIT:C91060"
          label: "Centimeters of Water"
        value: 14.0
      interval:
        start: "2020-03-22T00:00:00Z"
        end: "2020-03-28T00:00:00Z"
- treatment:
    agent:
      id: "NCIT:C84217"
      label: "Tocilizumab"
    doseIntervals:
    - interval:
        start: "2020-03-24T00:00:00Z"
        end: "2020-03-28T00:00:00Z"

metaData

The MetaData is required to provide details about all of the ontologies and external references used in the Phenopacket.

metaData:
  resources:
  - id: "ncit"
    name: "NCI Thesaurus OBO Edition"
    url: "http://purl.obolibrary.org/obo/ncit.owl"
    version: "http://purl.obolibrary.org/obo/ncit/releases/2019-11-26/ncit.owl"
    namespacePrefix: "NCIT"
  - id: "mondo"
    name: "Mondo Disease Ontology"
    url: "http://purl.obolibrary.org/obo/mondo.obo"
    namespacePrefix: "MONDO"
  - id: "doi"
    name: "Digital Object Identifier"
    url: "http://dx.doi.org"
    namespacePrefix: "DOI"
  - id: "pubmed"
    name: "PubMed"
    url: "https://pubmed.ncbi.nlm.nih.gov/"
    namespacePrefix: "PUBMED"
  phenopacketSchemaVersion: "2.0"
  externalReferences:
  - id: "DOI:10.1016/j.jaccas.2020.04.001"
    reference: "PMID:32292915"
    description: "The Imperfect Cytokine Storm: Severe COVID-19 With ARDS in a Patient\
      \ on Durable LVAD Support"