FHIR API - JupyterHealth Software

The JHE FHIR server is served at FHIR/R5/ (the lowercase alias fhir/r5/ is also supported for backward compatibility).

Querying: JHE-native vs imported¶

Every search hits one store, selected by _source:

no _source → JHE-native records (the default)
_source=https://jupyterhealth.org/fhir/fhir-source/90001 → one imported FHIR Source
_source:below=https://jupyterhealth.org/fhir/fhir-source/ → all imported resources

GET /FHIR/R5/Observation?patient=40001                                            # JHE-native (default)
GET /FHIR/R5/Condition?_source=https://jupyterhealth.org/fhir/fhir-source/90001    # one source
GET /FHIR/R5/Condition?_source:below=https://jupyterhealth.org/fhir/fhir-source/   # all imported

JHE-native records carry meta.source: "https://jupyterhealth.org/jhe".
Imported records carry meta.source: "https://jupyterhealth.org/fhir/fhir-source/<id>".
A single query never spans both stores.

Filtering, sorting & counting¶

Search parameters (US Core) — the set available depends on the resource type:

Type	Examples
token	`?clinical-status=active` · `?code=http://loinc.org\|1234-5` · `?category=problem-list-item`
date	`?recorded-date=ge2024-01-01` · `?date=le2024-12-31` (`ge`/`le`/`gt`/`lt` or a bare date)
string (starts-with)	`?name=nor` matches “North Clinic” (case-insensitive)
reference	`?encounter=Encounter/abc` · `?patient=40001`

comma = OR: ?category=problem-list-item,encounter-diagnosis
repeat = AND / range: ?recorded-date=ge2024-01-01&recorded-date=le2024-12-31
always available on any resource: ?_id=… · ?_lastUpdated=ge2024-01-01

Sort with _sort (prefix - for descending):

GET /FHIR/R5/Observation?patient=40001&_sort=date          # by effective[x], oldest first
GET /FHIR/R5/Condition?patient=40001&_sort=-_lastUpdated    # most recently updated first

_sort=date → the resource’s date (Observation effective[x], Condition recordedDate, MedicationRequest authoredOn, …)
_sort=_lastUpdated → record update time

Count only with _summary=count:

// GET /FHIR/R5/Condition?patient=40001&_summary=count
{
  "resourceType": "Bundle",
  "type": "searchset",
  "total": 12,
  "entry": []
}

Working with OMH Observations¶

OMH Observations are the primary data type in JHE and are stored natively in the system. They are read and written as FHIR R5 resources.

Querying Observations¶

Patient-scoping parameters are optional — a paramless search returns everything you can access (a patient user’s own observations; a practitioner’s observations across all their organizations). When filtering by study (patient._has:Group:member:_id), results are additionally restricted to the study’s consented observation codes.

Query Parameter	Example	Description
`patient._has:Group:member:_id`	`30001`	Observations for patients enrolled in Study 30001
`patient`	`40001`	Observations for Patient 40001
`patient.organization`	`20001`	Observations for patients in Organization 20001
`patient.identifier`	`http://ehr.example.com\|abc123`	Observations for the patient with that identifier
`code`	`https://w3id.org/openmhealth\|omh:blood-pressure:4.0`	Filter by observation type
`date`	`ge2024-01-01`	Filter by `effective[x]` time (`ge`/`le`/`gt`/`lt`)

Notes:

subject.reference references a Patient ID
device.reference references a Data Source (Device) ID
valueAttachment.data is Base64-encoded JSON

Examples:

# all blood-pressure observations for a patient
GET /FHIR/R5/Observation?patient=40001&code=https://w3id.org/openmhealth|omh:blood-pressure:4.0

# a study's observations, most recent effective time first
GET /FHIR/R5/Observation?patient._has:Group:member:_id=30001&_sort=-date

# newer than a given effective time (filters on effective[x] — see Effective Time below)
GET /FHIR/R5/Observation?patient=40001&date=gt2026-01-01

# an effective-time window (repeat = AND)
GET /FHIR/R5/Observation?patient=40001&date=ge2026-01-01&date=le2026-06-30

# two observation types at once (comma = OR)
GET /FHIR/R5/Observation?patient=40001&code=omh:blood-pressure:4.0,omh:heart-rate:2.0

# just the count
GET /FHIR/R5/Observation?patient=40001&_summary=count

// GET /FHIR/R5/Observation?patient._has:Group:member:_id=30001&code=https://w3id.org/openmhealth|omh:blood-pressure:4.0
{
  "resourceType": "Bundle",
  "type": "searchset",
  "entry": [
    {
      "resource": {
        "resourceType": "Observation",
        "id": "63416",
        "meta": {
          "lastUpdated": "2024-10-25T21:14:02.871132+00:00"
        },
        "identifier": [
          {
            "value": "6e3db887-4a20-3222-9998-2972af6fb091",
            "system": "https://ehr.example.com"
          }
        ],
        "status": "final",
        "subject": {
          "reference": "Patient/40001"
        },
        "device": {
          "reference": "Device/70001"
        },
        "code": {
          "coding": [
            {
              "code": "omh:blood-pressure:4.0",
              "system": "https://w3id.org/openmhealth"
            }
          ]
        },
        "valueAttachment": {
          "data": "eyJoZWFkZXIiOnsidXVpZCI6IjZlM2RiODg3LTRhMjAtMzIyMi05OTk4LTI5NzJhZjZmYjA5MSIsInNjaGVtYV9pZCI6eyJuYW1lc3BhY2UiOiJvbWgiLCJuYW1lIjoiYmxvb2QtcHJlc3N1cmUiLCJ2ZXJzaW9uIjoiNC4wIn0sInNvdXJjZV9jcmVhdGlvbl9kYXRlX3RpbWUiOiIyMDIxLTAzLTE0VDA5OjI1OjAwLTA3OjAwIn0sImJvZHkiOnsic3lzdG9saWNfYmxvb2RfcHJlc3N1cmUiOnsidmFsdWUiOjE0MiwidW5pdCI6Im1tSGcifSwiZGlhc3RvbGljX2Jsb29kX3ByZXNzdXJlIjp7InZhbHVlIjo4OSwidW5pdCI6Im1tSGcifSwiZWZmZWN0aXZlX3RpbWVfZnJhbWUiOnsiZGF0ZV90aW1lIjoiMjAyMS0wMy0xNFQwOToyNTowMC0wNzowMCJ9fX0=",
          "contentType": "application/json"
        }
      }
    },
    ...

Uploading Observations¶

Observations are uploaded as FHIR Batch Bundles via POST to the base endpoint.

// POST /FHIR/R5/
{
  "resourceType": "Bundle",
  "type": "batch",
  "entry": [
    {
      "resource": {
        "resourceType": "Observation",
        "status": "final",
        "code": {
          "coding": [
            {
              "system": "https://w3id.org/openmhealth",
              "code": "omh:blood-pressure:4.0"
            }
          ]
        },
        "subject": {
          "reference": "Patient/40001"
        },
        "device": {
          "reference": "Device/70001"
        },
        "identifier": [
          {
            "value": "6e3db887-4a20-3222-9998-2972af6fb091",
            "system": "https://ehr.example.com"
          }
        ],
        "valueAttachment": {
          "contentType": "application/json",
          "data": "eyJoZWFkZXIiOnsidXVpZCI6IjZlM2RiODg3LTRhMjAtMzIyMi05OTk4LTI5NzJhZjZmYjA5MSIsInNjaGVtYV9pZCI6eyJuYW1lc3BhY2UiOiJvbWgiLCJuYW1lIjoiYmxvb2QtcHJlc3N1cmUiLCJ2ZXJzaW9uIjoiNC4wIn0sInNvdXJjZV9jcmVhdGlvbl9kYXRlX3RpbWUiOiIyMDIxLTAzLTE0VDA5OjI1OjAwLTA3OjAwIn0sImJvZHkiOnsic3lzdG9saWNfYmxvb2RfcHJlc3N1cmUiOnsidmFsdWUiOjE0MiwidW5pdCI6Im1tSGcifSwiZGlhc3RvbGljX2Jsb29kX3ByZXNzdXJlIjp7InZhbHVlIjo4OSwidW5pdCI6Im1tSGcifSwiZWZmZWN0aXZlX3RpbWVfZnJhbWUiOnsiZGF0ZV90aW1lIjoiMjAyMS0wMy0xNFQwOToyNTowMC0wNzowMCJ9fX0="
        }
      },
      "request": {
        "method": "POST",
        "url": "Observation"
      }
    },
    ...

Effective Time¶

On upload, JHE lifts the OMH body.effective_time_frame out of the Base64 payload and onto indexed columns so observations can be queried by time. These columns are surfaced on read as FHIR R5 Observation.effective[x]. The valueAttachment.data blob remains the source of truth; the elevated values are a derived projection, so a missing or unrecognised time frame simply leaves the row without an effective[x] value.

A single point in time becomes effectiveDateTime; every OMH time_interval form becomes an effectivePeriod (start + end):

OMH `effective_time_frame` shape	Example	FHIR R5 output
`date_time`	`{ "date_time": "2026-07-18T09:30:00+09:00" }`	`effectiveDateTime: "2026-07-18T09:30:00+09:00"`
`time_interval` — `start` + `end`	`{ "start_date_time": "…T09:00…", "end_date_time": "…T10:00…" }`	`effectivePeriod: { start, end }`
`time_interval` — `start` + `duration`	`{ "start_date_time": "…T09:00…", "duration": { "value": 60, "unit": "min" } }`	`effectivePeriod: { start, end }` (end = start + duration)
`time_interval` — `end` + `duration`	`{ "end_date_time": "…T10:00…", "duration": { "value": 60, "unit": "min" } }`	`effectivePeriod: { start, end }` (start = end − duration)
`time_interval` — `date` + `part_of_day`	`{ "date": "2026-07-18", "part_of_day": "morning" }`	`effectivePeriod: { start, end }` (the part-of-day window)

Notes:

Timezone: a datetime with no offset is interpreted as UTC, matching the legacy OMH convention.
Duration units are drawn from the OMH duration value set (ps, ns, us, ms, sec, min, h, d, wk, Mo, yr); calendar units (Mo, yr) are added relative to the anchor date (e.g. Jan 31 + 1 month → Feb 28).
part_of_day maps to a fixed window on the given day: morning 06:00–12:00, afternoon 12:00–18:00, evening 18:00–24:00, night 00:00–06:00.
After a round-trip through storage, datetimes are returned in UTC (e.g. +00:00); this is the same instant, and the original offset is retained in valueAttachment.data.

Working with Patients, Practitioners, Organizations, Groups (Studies) and Devices (Data Sources)¶

These resources are read-only projections of JHE system entities — writes to them via FHIR are not supported (use the /api/v1/ REST API to manage these). All support the same patient-scoping query parameters.

Query Parameter	Example	Description
`_has:Group:member:_id`	`30001`	Resources belonging to patients in Study 30001
`patient`	`40001`	Resources belonging to Patient 40001
`patient.organization`	`20001`	Resources belonging to patients in Organization 20001
`patient._has:Group:member:_id`	`30001`	Resources belonging to patients enrolled in Study 30001
`patient.identifier`	`http://ehr.example.com\|abc123`	Resources belonging to the patient with that identifier
`identifier`	`http://ehr.example.com\|abc123`	Match the resource itself by identifier (Patient only)
`family` / `given` / `name`	`Smith`	Patient name starts-with, case-insensitive (Patient only)
`birthdate`	`ge1980-01-01`	Patient date of birth (Patient only)

// GET /FHIR/R5/Patient?_has:Group:member:_id=30001
{
  "resourceType": "Bundle",
  "type": "searchset",
  "entry": [
    {
      "resource": {
        "resourceType": "Patient",
        "id": "40001",
        "meta": {
          "lastUpdated": "2024-10-23T12:35:25.142027+00:00"
        },
        "identifier": [
          {
            "value": "fhir-1234",
            "system": "http://ehr.example.com"
          }
        ],
        "name": [
          {
            "given": ["Peter"],
            "family": "ThePatient"
          }
        ],
        "birthDate": "1980-01-01",
        "telecom": [
          {
            "value": "peter@example.com",
            "system": "email"
          },
          {
            "value": "347-111-1111",
            "system": "phone"
          }
        ]
      }
    },
    ...

The same scoping parameters apply to Group (Study), Device (Data Source), Organization, and Practitioner:

Resource	Query	Returns
`Group` (Study)	`GET /FHIR/R5/Group?patient._has:Group:member:_id=30001`	The study with ID 30001
`Group` (Study)	`GET /FHIR/R5/Group?patient=40001`	Studies Patient 40001 is enrolled in
`Group` (Study)	`GET /FHIR/R5/Group?patient.organization=20001`	Studies in Organization 20001
`Device` (Data Source)	`GET /FHIR/R5/Device?patient._has:Group:member:_id=30001`	Data sources used in Study 30001
`Device` (Data Source)	`GET /FHIR/R5/Device?patient=40001`	Data sources used in Patient 40001’s studies
`Device` (Data Source)	`GET /FHIR/R5/Device?patient.organization=20001`	Data sources in studies under Organization 20001
`Organization`	`GET /FHIR/R5/Organization?patient._has:Group:member:_id=30001`	The organization backing Study 30001
`Organization`	`GET /FHIR/R5/Organization?patient=40001`	Organizations Patient 40001 belongs to
`Organization`	`GET /FHIR/R5/Organization?patient.organization=20001`	Organization 20001
`Practitioner`	`GET /FHIR/R5/Practitioner?patient._has:Group:member:_id=30001`	Practitioners in Study 30001’s organization
`Practitioner`	`GET /FHIR/R5/Practitioner?patient=40001`	Practitioners in Patient 40001’s organizations
`Practitioner`	`GET /FHIR/R5/Practitioner?patient.organization=20001`	Practitioners in Organization 20001

Working with other resources¶

Any FHIR resource type not natively modeled in JHE (such as QuestionnaireResponse, Condition, or MedicationRequest) can be stored and retrieved via the auxiliary resource store. Before uploading, a patient must register a FHIR Source that identifies the upstream system the data originates from.

Step 1: Register a FHIR Source¶

POST /api/v1/fhir_sources
Authorization: Bearer WMSk9Te6QpENVxudxkRjeNBFlCf5pq
Content-Type: application/json
Accept: application/json

{
  "data_source": 70005,
  "label": "Neptune MyChart",
  "fhir_base_url": "https://fhir.neptune.org/api/FHIR/R4"
}

Response:

{
  "id": 90001,
  "patient": 40001,
  "dataSource": 70005,
  "label": "Neptune MyChart",
  "fhirBaseUrl": "https://fhir.neptune.org/api/FHIR/R4",
  "lastUpdated": "2026-06-07T04:11:52.577605Z"
}

The id returned (90001) is the FHIR Source ID used in subsequent requests.

Step 2: Upload the resource¶

Name the FHIR Source one of two ways (omit both → 400):

Preferred — set meta.source on the resource body:

"meta": { "source": "https://jupyterhealth.org/fhir/fhir-source/90001" }

Or — send the X-JHE-FHIR-Source-ID header (a convenience fallback; wins if both are present):
```
X-JHE-FHIR-Source-ID: 90001
```

POST /FHIR/R5/QuestionnaireResponse
Authorization: Bearer WMSk9Te6QpENVxudxkRjeNBFlCf5pq
Content-Type: application/json
Accept: application/json
X-JHE-FHIR-Source-ID: 90001

{
  "resourceType": "QuestionnaireResponse",
  "status": "completed",
  "questionnaire": "Questionnaire/weekly-symptom-severity-vas",
  "subject": {
    "reference": "Patient/123"
  },
  "authored": "2026-05-28T14:30:00Z",
  "item": [
    {
      "linkId": "cough-severity",
      "answer": [{"valueInteger": 37}]
    },
    {
      "linkId": "dyspnea-severity",
      "answer": [{"valueInteger": 62}]
    },
    {
      "linkId": "fatigue-severity",
      "answer": [{"valueInteger": 48}]
    }
  ]
}

Response:

{
  "resourceType": "QuestionnaireResponse",
  "id": "2d50b34d-b33c-4f47-a5e8-595764d51f53",
  "status": "completed",
  "questionnaire": "Questionnaire/weekly-symptom-severity-vas",
  "subject": {
    "reference": "Patient/123"
  },
  "authored": "2026-05-28T14:30:00Z",
  "item": [
    {
      "linkId": "cough-severity",
      "answer": [{"valueInteger": 37}]
    },
    {
      "linkId": "dyspnea-severity",
      "answer": [{"valueInteger": 62}]
    },
    {
      "linkId": "fatigue-severity",
      "answer": [{"valueInteger": 48}]
    }
  ]
}

The id returned is a UUID assigned by JHE.

Step 3: Retrieve the resource¶

Retrieve by FHIR Source, by patient/study, or by resource ID. (The X-JHE-FHIR-Source-ID header is write-only — it is ignored on reads; select a source with _source instead.)

From one FHIR Source:

GET /FHIR/R5/QuestionnaireResponse?_source=https://jupyterhealth.org/fhir/fhir-source/90001

From all imported sources:

GET /FHIR/R5/QuestionnaireResponse?_source:below=https://jupyterhealth.org/fhir/fhir-source/

By patient or study (add any filter/sort from Filtering, sorting & counting):

GET /FHIR/R5/QuestionnaireResponse?patient=40001
GET /FHIR/R5/QuestionnaireResponse?patient._has:Group:member:_id=30001&status=completed&_sort=-date

By resource ID:

GET /FHIR/R5/QuestionnaireResponse/2d50b34d-b33c-4f47-a5e8-595764d51f53

All reads return a FHIR searchset Bundle (or a single resource for an ID lookup).