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Tutorial - FHIR Encounter Resource ​

Background ​

Scenario ​

John Thompson finally arrives at the clinical center and has just started his visit with the practitioner Kelly Smith. He told Kelly abount his concerns about fever and high blood pressure. So, Kelly checked the current temperature and the blood pressure: 96.8 F and 130/80. Kelly diagnosed hypertension and requested some blood tests to diagnose the cause of the fever.

Let's create an Encounter to track the visit.

Setup environment ​

  • Same to Tutorial 02

Introduction ​

Import library ​

At the beginning we need to import libraries fhirpy and os.

Also, we re-use the customise function pprint from Tutorial-02. We'll use it to display some Observation resource data structures.

py
import os
from fhirpy import AsyncFHIRClient
import os
from fhirpy import AsyncFHIRClient

Create an instance of connection ​

To load data from FHIR server we should instaniate FHIRClient class from fhirpy AsyncFHIRClient method.

Let's pass url and authorization arguments from environment.

py
client = AsyncFHIRClient(
        url='http://localhost:8080/fhir/',
        authorization='Bearer TOKEN',
    )
client = AsyncFHIRClient(
        url='http://localhost:8080/fhir/',
        authorization='Bearer TOKEN',
    )

Now, we are able to operate with FHIR resources using client.

  • Before creating Encounter resource we need to find the patient -John Thompson.
py
patient = await client.resources('Patient').search(
    name=['John', 'Thompson']
).first()

pprint(patient)
patient = await client.resources('Patient').search(
    name=['John', 'Thompson']
).first()

pprint(patient)
  • Next we need to find the parctitioner - Kelly Smith
py
practitioner = await client.resources('Patient').search(
    name=['Kelly', 'Smith']
).first()

pprint(practitioner)
practitioner = await client.resources('Patient').search(
    name=['Kelly', 'Smith']
).first()

pprint(practitioner)

The clinical center where our patient has finally arrived is Hahnemann University Hospital

  • Find Location resource for the clinical center 'Hahnemann University Hospital'
py
location = await client.resources('Location').search(
    name='Hahnemann University Hospital'
).first()

pprint(location)
location = await client.resources('Location').search(
    name='Hahnemann University Hospital'
).first()

pprint(location)

And finally load Appointment that scheduled this Encounter.

py
appointment = await client.resources('Appointment').search(actor=patient['id']).first()

pprint(appointment)
appointment = await client.resources('Appointment').search(actor=patient['id']).first()

pprint(appointment)

Encounter Resource ​

Encounter is an interaction between a patient and healthcare provider for the purpose of providing healthcare service or assessing the health status of a patient.

An Encounter encompasses the lifecycle from pre-admission, the actual encounter, admission, stay and discharge. During the encounter the patient may move from practitioner to practitioner and location to location.

Encounter has a broad scope, so some components may be irrelevant to a specific context, the class element is used to distinguish between settings.

Differnt organizations may have different lebel of aggregation for Encounter. For example, during hospitalization each single visit of a practitioner may lead to a new instance of Encounter, but in other organization the whole hospitalization may be defined in terms of a single Encounter.

We use Appointment for the planning stage. When the appointment is about to start, we create a new Encounter and mark Appointment object as fulfilled.

Load Encounter resource ​

Let's search for existent Encounter resources before creating one.

py
encounters = await client.resources('Encounter').search(subject=patient['id']).first()

pprint(encounters)
encounters = await client.resources('Encounter').search(subject=patient['id']).first()

pprint(encounters)

Create Condition ​

Condition resource can be used to describe information about illness identified from application of clinical reasoning. It is important to distinguish Condition from Observation, we use Observation when a symptom contributes to the establishment of a condition. Condition on the other hand is about a clinician's assessment and assertion of a particular aspect of a patient's state of healt.

Let's create Condition for hypertension. Hypertension is encoded as 38341003 in http://snomed.info/sct system.

py
condition = client.resource(
    'Condition',
    code={
        'coding':[{
            'system': 'http://snomed.info/sct',
            'code':'38341003'
        }]
    },
    subject=patient.to_reference()
)

pprint(condition)
condition = client.resource(
    'Condition',
    code={
        'coding':[{
            'system': 'http://snomed.info/sct',
            'code':'38341003'
        }]
    },
    subject=patient.to_reference()
)

pprint(condition)

Create Encounter ​

Now that we've all the information required, we can finally register our Encounter.

py
encounter = client.resource(
    'Encounter',
    status='in-progress',
    subject=patient.to_reference(),
    participant=[{
        'type':[{
            'coding':[{
                'system': 'http://hl7.org/fhir/v3/ParticipationType',
                'code': 'PPRF'
            }]
        }],
        'individual': practitioner
    }],
    appointment=appointment.to_reference(),
    diagnosis=[{'condition':condition}],
    location=[{'location','status':'active'}]
)

pprint(encounter)
encounter = client.resource(
    'Encounter',
    status='in-progress',
    subject=patient.to_reference(),
    participant=[{
        'type':[{
            'coding':[{
                'system': 'http://hl7.org/fhir/v3/ParticipationType',
                'code': 'PPRF'
            }]
        }],
        'individual': practitioner
    }],
    appointment=appointment.to_reference(),
    diagnosis=[{'condition':condition}],
    location=[{'location','status':'active'}]
)

pprint(encounter)

Register symptoms with Observation ​

We can link Observation resource to Encounter with Observation.context.

Base on scenario to register the observations:

  • temperature 96.8F
  • blood pressure 130/80

And link them to the encounter we've just created.

py
temperature_observation = client.resource(
    'Observation',
    status='preliminary',
    category=[{
        'coding':[{
            'system': 'http://hl7.org/fhir/observation-category',
            'code': 'vital-signs'
        }]
    }],
    code={
        'coding':[{
            'system': 'http://loinc.org',
            'code': '8310-5'
        }]
    },
    effectiveDateTime='2018-09-16',
    valueQuantity={
        'system': 'http://unitsofmeasure,org',
        'value': 96.8,
        'code': 'degF'
    },
    encounter=encounter.to_reference(),
    subject=patient.to_reference()
)
temperature_observation = client.resource(
    'Observation',
    status='preliminary',
    category=[{
        'coding':[{
            'system': 'http://hl7.org/fhir/observation-category',
            'code': 'vital-signs'
        }]
    }],
    code={
        'coding':[{
            'system': 'http://loinc.org',
            'code': '8310-5'
        }]
    },
    effectiveDateTime='2018-09-16',
    valueQuantity={
        'system': 'http://unitsofmeasure,org',
        'value': 96.8,
        'code': 'degF'
    },
    encounter=encounter.to_reference(),
    subject=patient.to_reference()
)
  • Create blood pressure Observation resource instance
py
blood_pressure_observation = client.resource(
    'Observation',
    id='blood_pressure_observation_for_john_thompson',
    status='preliminary',
    category=[{
        'coding':[{
            'system': 'http://hl7.org/fhir/observation-catagory',
            'code': 'vital-signs'
        }]
    }],
    code={
        'coding':[{
            'system':'http://loinc.org',
            'code': '55284-4'
        }]
    },
    effectiveDateTime='2018-09-16',
    encounter=encounter.to_reference(),
    subject=patient.to_reference()
)

pprint(blood_pressure_observation)
blood_pressure_observation = client.resource(
    'Observation',
    id='blood_pressure_observation_for_john_thompson',
    status='preliminary',
    category=[{
        'coding':[{
            'system': 'http://hl7.org/fhir/observation-catagory',
            'code': 'vital-signs'
        }]
    }],
    code={
        'coding':[{
            'system':'http://loinc.org',
            'code': '55284-4'
        }]
    },
    effectiveDateTime='2018-09-16',
    encounter=encounter.to_reference(),
    subject=patient.to_reference()
)

pprint(blood_pressure_observation)

Summary ​

In this tutorial we've discussed:

  • How to search for Encounter
  • How to create Condition
  • What is the difference between Condition and Observation
  • How to create Encounter
  • How to link Condition and Observation to Encounter

Acknowledgement ​

Aidbox / jupyter-course

fhirpy