Skip to content

DeptSaludPR/BioPortal-FHIR

BranchesTags

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

5 Commits
README.md
README.md
 
 

Repository files navigation

BioPortal

Test Results

BioPortal currently collects the following fields for the test results:

Field Name Data Type
Order ID string
Patient Patient
Laboratory Laboratory
Ordered By Entity
Processed By Entity

Patient

Click to expand!
Field Name Data Type
Patient ID string
SSN string
First Name string
Middle Name string
Last Name string
Second Last Name string
Birth Date Date
Sex string
Is Pregnant boolean
Pregnant Gestation Weeks int
Pregnant Estimated Birth Date Date
Pregnant Obstetrician string
Is First Responder boolean
Is Homeless boolean
Is In Nursing Home boolean
Address Address
Country Iso2 Code
Phone Number 1 string
Phone Number 2 string
Work Name string
Work Address Address
Marital Status string
Primary Language string
Deceased boolean
Primary Practitioner Entity

Laboratory

Click to expand!
Field Name Data Type
Has Symptoms boolean
Onset Date Date
Symptoms string[] - Symptoms
Sample Collected Date DateTime UTC
Result Reported Date DateTime UTC
Sample Type string
Test LOINC string
Result SNOMED string
Result File LOINC string

Entity

Click to expand!
Field Name Data Type
Entity ID UUID
Entity External ID string
Name string
Address Address
Phone Number string

Address

Click to expand!
Field Name Data Type
AddressLine1 string
AddressLine2 string
City string
State string - 2 letter Code
Country Iso2 Code

Send Test Results via HL7 FHIR

BioPortal provides a standarized way to receive test result information utilizing HL7 FHIR .

HL7 FHIR Resources

The resources utilized for sending test results are the following:

HL7 FHIR Bundle

One laboratory test result will consist of an HL7 FHIR Bundle with multiple resources.

Bundle will include:

  • Diagnostic Report
  • Patient
  • Pregnancy Observation
  • Homeless Condition
  • First Responder Condition
  • Nursing Home Condition
  • Symptoms Conditions (0 to X)
  • Specimen
  • Result Observation (0 to X)

Example:

{
  "resourceType": "Bundle",
  "meta": {
    "tag": [
      {
        "system": "http://terminology.hl7.org/CodeSystem/v3-ObservationValue",
        "code": "SUBSETTED",
        "display": "Resource encoded in summary mode"
      }
    ]
  },
  "type": "collection",
  "entry": [
    {
      "resource": {
        "resourceType": "DiagnosticReport",
        "id": "gn-174580",
        "meta": {
          "tag": [
            {
              "system": "http://terminology.hl7.org/CodeSystem/v3-ObservationValue",
              "code": "SUBSETTED",
              "display": "Resource encoded in summary mode"
            }
          ]
        },
        "extension": [
          {
            "url": "https://bioportal.salud.gov.pr/fhir/r4/StructureDefinition/ordered-by",
            "valueReference": {
              "reference": "Organization/urn:uuid:880bf5c8-1af9-45a3-ac6c-3ba96276355d"
            }
          }
        ],
        "identifier": [
          {
            "value": "gn-174580"
          }
        ],
        "basedOn": [
          {
            "reference": "ServiceRequest/gn-174580"
          }
        ],
        "status": "final",
        "code": {
          "coding": [
            {
              "system": "LN",
              "code": "94500-6"
            }
          ]
        },
        "subject": {
          "reference": "Patient/100741232"
        },
        "issued": "2020-09-07T02:01:14.480-04:00",
        "performer": [
          {
            "reference": "Organization/urn:uuid:880bf5c8-1af9-45a3-ac6c-3ba96276355d",
            "display": "Laboratorio Clinico Toledo"
          }
        ],
        "resultsInterpreter": [
          {
            "reference": "Practitioner/1124085790"
          }
        ],
        "specimen": [
          {
            "reference": "Specimen/580128"
          }
        ],
        "result": [
          {
            "reference": "Observation/urn:uuid:2d6711f6-c5ba-494c-9e4b-968c8f51ce83"
          }
        ]
      },
      "request": {
        "method": "POST",
        "url": "DiagnosticReport"
      }
    },
    {
      "resource": {
        "resourceType": "ServiceRequest",
        "id": "gn-174580",
        "meta": {
          "tag": [
            {
              "system": "http://terminology.hl7.org/CodeSystem/v3-ObservationValue",
              "code": "SUBSETTED",
              "display": "Resource encoded in summary mode"
            }
          ]
        },
        "identifier": [
          {
            "value": "gn-174580"
          }
        ],
        "status": "completed",
        "code": {
          "coding": [
            {
              "system": "http://loinc.org",
              "code": "94500-6"
            }
          ]
        },
        "subject": {
          "reference": "Patient/100741232"
        },
        "requester": {
          "reference": "Practitioner/1124085790"
        },
        "performer": [
          {
            "reference": "Organization/urn:uuid:880bf5c8-1af9-45a3-ac6c-3ba96276355d",
            "display": "Laboratorio Clinico Toledo"
          }
        ],
        "reasonCode": [
          {
            "coding": [
              {
                "system": "ICD-10-CM",
                "code": "U07.2",
                "display": "COVID-19, virus not identified"
              }
            ]
          }
        ]
      },
      "request": {
        "method": "POST",
        "url": "ServiceRequest"
      }
    },
    {
      "fullUrl": "Patient/100741232",
      "resource": {
        "resourceType": "Patient",
        "id": "100741232",
        "meta": {
          "tag": [
            {
              "system": "http://terminology.hl7.org/CodeSystem/v3-ObservationValue",
              "code": "SUBSETTED",
              "display": "Resource encoded in summary mode"
            }
          ]
        },
        "identifier": [
          {
            "system": "urn:mrns",
            "value": "100741232"
          }
        ],
        "name": [
          {
            "family": "Nieves Miranda",
            "given": ["Elvis"]
          }
        ],
        "telecom": [
          {
            "system": "phone",
            "value": "7871234567",
            "use": "home"
          }
        ],
        "gender": "male",
        "birthDate": "1990-01-01",
        "address": [
          {
            "line": ["Calle Test"],
            "city": "San Juan",
            "state": "Puerto Rico",
            "postalCode": "00921"
          }
        ]
      },
      "request": {
        "method": "POST",
        "url": "Patient",
        "ifNoneExist": "identifier=12345"
      }
    },
    {
      "resource": {
        "resourceType": "Observation",
        "id": "urn:uuid:2d6711f6-c5ba-494c-9e4b-968c8f51ce83",
        "meta": {
          "tag": [
            {
              "system": "http://terminology.hl7.org/CodeSystem/v3-ObservationValue",
              "code": "SUBSETTED",
              "display": "Resource encoded in summary mode"
            }
          ]
        },
        "status": "final",
        "category": [
          {
            "coding": [
              {
                "system": "http://terminology.hl7.org/CodeSystem/observation-category",
                "code": "laboratory",
                "display": "laboratory"
              }
            ]
          }
        ],
        "code": {
          "coding": [
            {
              "system": "http://loinc.org",
              "code": "94500-6",
              "display": "SARS-CoV-2 (NAA) by PCR"
            }
          ]
        },
        "subject": {
          "reference": "Patient/100741232"
        },
        "issued": "2020-09-07T02:01:14.451-04:00",
        "performer": [
          {
            "reference": "Organization/urn:uuid:880bf5c8-1af9-45a3-ac6c-3ba96276355d",
            "display": "Laboratorio Clinico Test"
          }
        ],
        "valueCodeableConcept": {
          "coding": [
            {
              "system": "UNDEFINED",
              "code": "NOT_DETECTED",
              "display": "NOT_DETECTED"
            }
          ]
        }
      },
      "request": {
        "method": "POST",
        "url": "Observation"
      }
    },
    {
      "resource": {
        "resourceType": "Specimen",
        "id": "580128",
        "meta": {
          "tag": [
            {
              "system": "http://terminology.hl7.org/CodeSystem/v3-ObservationValue",
              "code": "SUBSETTED",
              "display": "Resource encoded in summary mode"
            }
          ]
        },
        "identifier": [
          {
            "value": "580128"
          }
        ],
        "type": {
          "text": "One swab received for PCR testing."
        },
        "receivedTime": "2020-07-28T17:16:34.77"
      },
      "request": {
        "method": "POST",
        "url": "Specimen"
      }
    },
    {
      "resource": {
        "resourceType": "Practitioner",
        "id": "1124085790",
        "meta": {
          "tag": [
            {
              "system": "http://terminology.hl7.org/CodeSystem/v3-ObservationValue",
              "code": "SUBSETTED",
              "display": "Resource encoded in summary mode"
            }
          ]
        },
        "identifier": [
          {
            "value": "1124085790"
          }
        ],
        "name": [
          {
            "family": "Test, MD.",
            "given": ["Juan"]
          }
        ],
        "telecom": [
          {
            "system": "phone"
          }
        ],
        "address": [
          {
            "line": [
              "Edif. Test",
              "Test Line 2"
            ],
            "state": "Puerto Rico",
            "country": "United States"
          }
        ]
      },
      "request": {
        "method": "POST",
        "url": "Practitioner"
      }
    },
    {
      "resource": {
        "resourceType": "Organization",
        "id": "urn:uuid:880bf5c8-1af9-45a3-ac6c-3ba96276355d",
        "meta": {
          "tag": [
            {
              "system": "http://terminology.hl7.org/CodeSystem/v3-ObservationValue",
              "code": "SUBSETTED",
              "display": "Resource encoded in summary mode"
            }
          ]
        },
        "name": "Laboratorio Clinico Test",
        "address": [
          {
            "line": ["Calle Test"],
            "city": "San Juan",
            "state": "Puerto Rico",
            "postalCode": "00921"
          }
        ]
      },
      "request": {
        "method": "POST",
        "url": "Organization"
      }
    }
  ]
}

HL7 FHIR Extensions

Diagnostic Report

Ordered By

{
  "url": "https://bioportal.salud.gov.pr/fhir/r4/StructureDefinition/ordered-by",
  "valueReference": "Reference(Organization)"
}

Patient

Mother’s Maiden Name

{
  "url": "http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName",
  "valueString": "Miranda"
}

Send Message

Endpoint

Purpose VERB URL
Send Covid-19 Test Results POST https://biolink.salud.gov.pr/fhir/r4

Authentication

Use the following HTTP headers

Header Value
Authorization ApiKey KEY

About

bioportal.salud.gov.pr/

Topics

government puerto-rico salud laboratory-automation covid-19 contact-tracing case-investigation

Resources

Readme
Activity
Custom properties

Stars

1 star

Watchers

3 watching

Forks

0 forks
Report repository

Releases

No releases published

Packages

No packages published