[
  {
    "phenotype_id": "PH1",
    "phenotype_version_id": 2,
    "name": "COVID-19 infection",
    "definition": "We ascertained people with a confirmed or suspected Covid-19 diagnosis as follows:\n\n\n1) a positive PCR or antigen test from the Covid-19 laboratory test data, with specimen date on or before 31 October 2020; or\n\n\n2) a Covid-19 diagnosis SNOMED-CT concept code appearing in the primary care data, with event date on or before 31 October; or\n\n\n3) a diagnosis ICD-10 code appearing in the hospital episodes (main or secondary diagnostic code position in the admitted patient care component of the hospital episode statistics), with admission date on or before 31 October or\n\n\n4) death registration with a mention (as underlying on contributing cause) of a diagnosis ICD-10 code , with death registration date on or before 31 October 2020.\n\n\n\n\n\n\n\n\n",
    "implementation": "",
    "publications": [],
    "validation": "",
    "citation_requirements": "",
    "created": "2021-10-06T15:58:48.523066Z",
    "author": "BHF CVD COVID UK Consortium",
    "collections": [
      {
        "name": "BHF Data Science Centre",
        "value": 20
      },
      {
        "name": "Phenotype Library",
        "value": 18
      }
    ],
    "tags": null,
    "organisation": {
      "id": 13,
      "slug": "bhf-data-science-centre",
      "name": "BHF Data Science Centre"
    },
    "world_access": 1,
    "updated": "2021-10-06T15:58:48.523092Z",
    "sex": [
      {
        "name": "Both",
        "value": "3"
      }
    ],
    "type": [
      {
        "name": "Disease or syndrome",
        "value": "2"
      }
    ],
    "trials": null,
    "ontology": null,
    "phenoflowid": "https://kclhi.org/phenoflow/workflows/github.com/phenoflow/COVID-19-infection---0ad8bf70-16ea-11ef-9de4-4d4ea830ad16/blob/read-potential-cases-fhir/COVID-19-infection.cwl",
    "data_sources": [
      {
        "name": "GPES Data for Pandemic Planning and Research (COVID-19)",
        "value": 1,
        "uid": "c7eed372-9f1e-467e-8a37-948f4de5abc4",
        "url": "https://healthdatagateway.org/en/dataset/874",
        "datasource_id": 874
      },
      {
        "name": "Hospital Episode Statistics Admitted Patient Care",
        "value": 2,
        "uid": "6599230a-df54-4615-937c-d724d239491f",
        "url": "https://healthdatagateway.org/en/dataset/875",
        "datasource_id": 875
      },
      {
        "name": "Civil Registration - Deaths",
        "value": 3,
        "uid": "b9009bc5-b7a6-4036-9d4b-a5133c0b14a3",
        "url": "https://healthdatagateway.org/en/dataset/877",
        "datasource_id": 877
      },
      {
        "name": "Covid-19 Second Generation Surveillance System",
        "value": 4,
        "uid": "4e289a0f-50e7-4413-9376-ffbd13fc1a59",
        "url": "https://healthdatagateway.org/en/dataset/854",
        "datasource_id": 854
      }
    ],
    "endorsements": null,
    "project_name": null,
    "coding_system": [
      {
        "name": "ICD10 codes",
        "value": 4
      },
      {
        "name": "SNOMED  CT codes",
        "value": 9
      }
    ],
    "corresp_author": null,
    "event_date_range": "01/01/2020 - 31/10/2020",
    "concept_information": [
      {
        "concept_id": 714,
        "concept_version_id": 2567,
        "concept_name": "COVID-19 infection - Primary Care",
        "coding_system": {
          "id": 9,
          "name": "SNOMED  CT codes",
          "description": "SNOMED CT codes"
        },
        "phenotype_id": "PH1",
        "phenotype_version_id": 2,
        "phenotype_name": "COVID-19 infection",
        "code_attribute_header": [
          "type"
        ],
        "codes": [
          {
            "code": "1008541000000105",
            "description": "Coronavirus ribonucleic acid detection assay (observable entity)",
            "attributes": {
              "type": "1"
            }
          },
          {
            "code": "1029481000000103",
            "description": "Coronavirus nucleic acid detection assay (observable entity) ",
            "attributes": {
              "type": "1"
            }
          },
          {
            "code": "120814005",
            "description": "Coronavirus antibody (substance) ",
            "attributes": {
              "type": "1"
            }
          },
          {
            "code": "1240391000000107",
            "description": "Antigen of severe acute respiratory syndrome coronavirus 2 (substance) ",
            "attributes": {
              "type": "1"
            }
          },
          {
            "code": "1240401000000105",
            "description": "Antibody to severe acute respiratory syndrome coronavirus 2 (substance) ",
            "attributes": {
              "type": "1"
            }
          },
          {
            "code": "1240421000000101",
            "description": "Serotype severe acute respiratory syndrome coronavirus 2 (qualifier value)",
            "attributes": {
              "type": "1"
            }
          },
          {
            "code": "1240511000000106",
            "description": "Detection of severe acute respiratory syndrome coronavirus 2 using polymerase chain reaction technique (procedure)",
            "attributes": {
              "type": "1"
            }
          },
          {
            "code": "1240521000000100",
            "description": "Otitis media caused by severe acute respiratory syndrome coronavirus 2 (disorder) ",
            "attributes": {
              "type": "1"
            }
          },
          {
            "code": "1240531000000103",
            "description": "Myocarditis caused by severe acute respiratory syndrome coronavirus 2 (disorder) ",
            "attributes": {
              "type": "1"
            }
          },
          {
            "code": "1240541000000107",
            "description": "Infection of upper respiratory tract caused by severe acute respiratory syndrome coronavirus 2 (disorder) ",
            "attributes": {
              "type": "1"
            }
          },
          {
            "code": "1240551000000105",
            "description": "Pneumonia caused by severe acute respiratory syndrome coronavirus 2 (disorder)",
            "attributes": {
              "type": "1"
            }
          },
          {
            "code": "1240561000000108",
            "description": "Encephalopathy caused by severe acute respiratory syndrome coronavirus 2 (disorder) ",
            "attributes": {
              "type": "1"
            }
          },
          {
            "code": "1240571000000101",
            "description": "Gastroenteritis caused by severe acute respiratory syndrome coronavirus 2 (disorder) ",
            "attributes": {
              "type": "1"
            }
          },
          {
            "code": "1240581000000104",
            "description": "Severe acute respiratory syndrome coronavirus 2 ribonucleic acid detected (finding)",
            "attributes": {
              "type": "1"
            }
          },
          {
            "code": "1240741000000103",
            "description": "Severe acute respiratory syndrome coronavirus 2 serology (observable entity) ",
            "attributes": {
              "type": "1"
            }
          },
          {
            "code": "1240751000000100",
            "description": "Coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 (disorder)",
            "attributes": {
              "type": "1"
            }
          },
          {
            "code": "1300631000000101",
            "description": "Coronavirus disease 19 severity score (observable entity) ",
            "attributes": {
              "type": "1"
            }
          },
          {
            "code": "1300671000000104",
            "description": "Coronavirus disease 19 severity scale (assessment scale) ",
            "attributes": {
              "type": "1"
            }
          },
          {
            "code": "1300681000000102",
            "description": "Assessment using coronavirus disease 19 severity scale (procedure) ",
            "attributes": {
              "type": "1"
            }
          },
          {
            "code": "1300721000000109",
            "description": "Coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 confirmed by laboratory test (situation)",
            "attributes": {
              "type": "1"
            }
          },
          {
            "code": "1300731000000106",
            "description": "Coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 confirmed using clinical diagnostic criteria (situation)",
            "attributes": {
              "type": "1"
            }
          },
          {
            "code": "1321181000000108",
            "description": "Coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 record extraction simple reference set (foundation metadata concept) ",
            "attributes": {
              "type": "1"
            }
          },
          {
            "code": "1321191000000105",
            "description": "Coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 procedures simple reference set (foundation metadata concept) ",
            "attributes": {
              "type": "1"
            }
          },
          {
            "code": "1321201000000107",
            "description": "Coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 health issues simple reference set (foundation metadata concept) ",
            "attributes": {
              "type": "1"
            }
          },
          {
            "code": "1321241000000105",
            "description": "Cardiomyopathy caused by severe acute respiratory syndrome coronavirus 2 (disorder) ",
            "attributes": {
              "type": "1"
            }
          },
          {
            "code": "1321301000000101",
            "description": "Severe acute respiratory syndrome coronavirus 2 ribonucleic acid qualitative existence in specimen (observable entity) ",
            "attributes": {
              "type": "1"
            }
          },
          {
            "code": "1321311000000104",
            "description": "Severe acute respiratory syndrome coronavirus 2 immunoglobulin M qualitative existence in specimen (observable entity) ",
            "attributes": {
              "type": "1"
            }
          },
          {
            "code": "1321321000000105",
            "description": "Severe acute respiratory syndrome coronavirus 2 immunoglobulin G qualitative existence in specimen (observable entity) ",
            "attributes": {
              "type": "1"
            }
          },
          {
            "code": "1321331000000107",
            "description": "Arbitrary concentration of severe acute respiratory syndrome coronavirus 2 total immunoglobulin in serum (observable entity) ",
            "attributes": {
              "type": "1"
            }
          },
          {
            "code": "1321341000000103",
            "description": "Arbitrary concentration of severe acute respiratory syndrome coronavirus 2 immunoglobulin G in serum (observable entity) ",
            "attributes": {
              "type": "1"
            }
          },
          {
            "code": "1321351000000100",
            "description": "Arbitrary concentration of severe acute respiratory syndrome coronavirus 2 immunoglobulin M in serum (observable entity) ",
            "attributes": {
              "type": "1"
            }
          },
          {
            "code": "1321541000000108",
            "description": "Severe acute respiratory syndrome coronavirus 2 immunoglobulin G detected (finding) ",
            "attributes": {
              "type": "1"
            }
          },
          {
            "code": "1321551000000106",
            "description": "Severe acute respiratory syndrome coronavirus 2 immunoglobulin M detected (finding) ",
            "attributes": {
              "type": "1"
            }
          },
          {
            "code": "1321761000000103",
            "description": "Severe acute respiratory syndrome coronavirus 2 immunoglobulin A detected (finding) ",
            "attributes": {
              "type": "1"
            }
          },
          {
            "code": "1322781000000102",
            "description": "Severe acute respiratory syndrome coronavirus 2 antigen detection result positive (finding) ",
            "attributes": {
              "type": "1"
            }
          },
          {
            "code": "1322871000000109",
            "description": "Severe acute respiratory syndrome coronavirus 2 antibody detection result positive (finding) ",
            "attributes": {
              "type": "1"
            }
          },
          {
            "code": "186747009",
            "description": "Coronavirus infection (disorder)",
            "attributes": {
              "type": "1"
            }
          }
        ]
      },
      {
        "concept_id": 715,
        "concept_version_id": 2569,
        "concept_name": "COVID-19 infection - Hospitalizations",
        "coding_system": {
          "id": 4,
          "name": "ICD10 codes",
          "description": "ICD10 Codes"
        },
        "phenotype_id": "PH1",
        "phenotype_version_id": 2,
        "phenotype_name": "COVID-19 infection",
        "code_attribute_header": [
          "type"
        ],
        "codes": [
          {
            "code": "U071",
            "description": "COVID-19, virus identified",
            "attributes": {
              "type": "1"
            }
          },
          {
            "code": "U072",
            "description": "COVID-19, virus not identified",
            "attributes": {
              "type": "1"
            }
          }
        ]
      }
    ],
    "status": 2,
    "doi": "https://doi.org/10.48533/wjmc-hh14",
    "is_deleted": null,
    "publish_status": 2,
    "owner": "ieuan.scanlon",
    "template": {
      "id": 2,
      "name": "BHF Data Science Centre Phenotype",
      "description": "BHF Data Science Centre Phenotype definitions that describe a list of clinical codes, algorithms using clinical codes, or set of clinical trials. Visit the BHF Data Science Centre website to learn more: https://bhfdatasciencecentre.org",
      "version_id": 1
    },
    "versions": [
      {
        "version_id": 2,
        "version_name": "COVID-19 infection",
        "version_date": "2021-10-06T15:58:48.704899Z",
        "is_published": true,
        "is_latest": true
      }
    ]
  }
]