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Phenopacket v2 (PXF)

PXF stands for Phenotype eXchange Format. Phenopackets v2 documentation.

Phenopackets v2

Figure extracted from www.ga4gh.org

Phenopackets organize information using top-level elements. Our software, Convert-Pheno, specifically processes data from the Phenopacket element, serialized in PXF format.

Browsing PXF JSON data

You can browse a public Phenopackets v2 file with onf of teh following JSON viewers:

PXF (Phenopacket top-element) as input PXF

When using the convert-pheno command-line interface, simply ensure the correct syntax is provided.

convert-pheno -ipxf ipxf.json -obff individuals.json
About JSON data structure in I/O files

Note that the input -ipxf file can consist of one individual (one JSON object) or a list of individuals (a JSON array of objects). The output --obff file will replicate the data structure of the input file.

About biosamples and interpretations

If these properties are present, they will be included in individuals.json within the info.phenopacket field as unprocessed data, as they are not mapped to any specific entity within the Beacon v2 Models. See additional info here.

The concept is to pass the necessary information as a hash (in Perl) or dictionary (in Python).

$bff = {
    data => $my_pxf_json_data,
    method => 'pxf2bff'
};

bff = {
     "data" : my_pxf_json_data,
     "method" : "pxf2bff"
}

The data will be sent as POST to the API's URL (see more info here). 

{
"data": {...}
"method": "pxf2bff"
}

Please find below examples of data:

{
   "diseases" : [],
   "id" : "phenopacket_id.AUNb6vNX1",
   "measurements" : [
      {
         "assay" : {
            "id" : "LOINC:35925-4",
            "label" : "BMI"
         },
         "value" : {
            "quantity" : {
               "unit" : {
                  "id" : "NCIT:C49671",
                  "label" : "Kilogram per Square Meter"
               },
               "value" : 26.63838307
            }
         }
      },
      {
         "assay" : {
            "id" : "LOINC:3141-9",
            "label" : "Weight"
         },
         "value" : {
            "quantity" : {
               "unit" : {
                  "id" : "NCIT:C28252",
                  "label" : "Kilogram"
               },
               "value" : 85.6358
            }
         }
      },
      {
         "assay" : {
            "id" : "LOINC:8308-9",
            "label" : "Height-standing"
         },
         "value" : {
            "quantity" : {
               "unit" : {
                  "id" : "NCIT:C49668",
                  "label" : "Centimeter"
               },
               "value" : 179.2973
            }
         }
      }
   ],
   "medicalActions" : [
      {
         "procedure" : {
            "code" : {
               "id" : "OPCS4:L46.3",
               "label" : "OPCS(v4-0.0):Ligation of visceral branch of abdominal aorta NEC"
            },
            "performed" : {
               "timestamp" : "1900-01-01T00:00:00Z"
            }
         }
      }
   ],
   "metaData" : null,
   "subject" : {
      "id" : "HG00096",
      "sex" : "MALE",
      "vitalStatus" : {
         "status" : "ALIVE"
      }
   }
}

{
  "ethnicity": {
    "id": "NCIT:C42331",
    "label": "African"
  },
  "id": "HG00096",
  "info": {
    "eid": "fake1"
  },
  "interventionsOrProcedures": [
    {
      "procedureCode": {
        "id": "OPCS4:L46.3",
        "label": "OPCS(v4-0.0):Ligation of visceral branch of abdominal aorta NEC"
      }
    }
  ],
  "measures": [
    {
      "assayCode": {
        "id": "LOINC:35925-4",
        "label": "BMI"
      },
      "date": "2021-09-24",
      "measurementValue": {
        "quantity": {
          "unit": {
            "id": "NCIT:C49671",
            "label": "Kilogram per Square Meter"
          },
          "value": 26.63838307
        }
      }
    },
    {
      "assayCode": {
        "id": "LOINC:3141-9",
        "label": "Weight"
      },
      "date": "2021-09-24",
      "measurementValue": {
        "quantity": {
          "unit": {
            "id": "NCIT:C28252",
            "label": "Kilogram"
          },
          "value": 85.6358
        }
      }
    },
    {
      "assayCode": {
        "id": "LOINC:8308-9",
        "label": "Height-standing"
      },
      "date": "2021-09-24",
      "measurementValue": {
        "quantity": {
          "unit": {
            "id": "NCIT:C49668",
            "label": "Centimeter"
          },
          "value": 179.2973
        }
      }
    }
  ],
  "sex": {
    "id": "NCIT:C20197",
    "label": "male"
  }
}