FHIR Resources

OmniEHR implements FHIR R4-compatible resources for comprehensive clinical data management. All resources follow HL7 FHIR specifications with standardized CRUD operations.

Supported Resources

OmniEHR supports the following FHIR R4 resources:

Patient

Demographics, identifiers, contact information

Observation

Vital signs, lab results, clinical measurements

Condition

Diagnoses, problems, health concerns

AllergyIntolerance

Allergies, intolerances, adverse reactions

MedicationRequest

Prescriptions, medication orders

Encounter

Clinical visits, episodes of care

Appointment

Scheduled appointments, bookings

Task

Care coordination, workflows, assignments

FHIR Capability Statement

OmniEHR exposes a FHIR CapabilityStatement at /api/fhir/metadata:

CapabilityStatement

{
  "resourceType": "CapabilityStatement",
  "status": "active",
  "date": "2026-03-04T10:30:00Z",
  "kind": "instance",
  "fhirVersion": "4.0.1",
  "format": ["json"],
  "software": {
    "name": "OmniEHR Core",
    "version": "2.0.0"
  },
  "implementation": {
    "description": "FHIR R4-compatible EHR API",
    "url": "https://your-server/api/fhir"
  },
  "rest": [
    {
      "mode": "server",
      "resource": [
        {
          "type": "Patient",
          "interaction": [
            { "code": "read" },
            { "code": "search-type" },
            { "code": "create" },
            { "code": "update" }
          ]
        }
        // ... additional resources
      ]
    }
  ]
}

Resource Details

Patient

Patient demographics and administrative information.

{
  "resourceType": "Patient",
  "id": "507f1f77bcf86cd799439011",
  "identifier": [
    {
      "system": "urn:pid",
      "value": "1000042"
    },
    {
      "system": "urn:mrn",
      "value": "MRN-12345"
    }
  ],
  "active": true,
  "name": [
    {
      "family": "Smith",
      "given": ["John"]
    }
  ],
  "telecom": [
    {
      "system": "phone",
      "value": "+1-555-0123"
    },
    {
      "system": "email",
      "value": "john.smith@example.com"
    }
  ],
  "gender": "male",
  "birthDate": "1980-01-15",
  "address": [
    {
      "line": ["123 Main St"],
      "city": "Springfield",
      "state": "IL",
      "postalCode": "62701"
    }
  ]
}

Interactions: read, search-type, create, update, $everything

Observation

Clinical observations including vital signs, lab results, and measurements.

{
  "resourceType": "Observation",
  "id": "507f1f77bcf86cd799439012",
  "status": "final",
  "code": {
    "coding": [
      {
        "system": "http://loinc.org",
        "code": "8480-6",
        "display": "Systolic blood pressure"
      }
    ]
  },
  "subject": {
    "reference": "Patient/507f1f77bcf86cd799439011"
  },
  "effectiveDateTime": "2026-03-04T10:30:00Z",
  "valueQuantity": {
    "value": 120,
    "unit": "mmHg",
    "system": "http://unitsofmeasure.org",
    "code": "mmHg"
  },
  "note": [
    {
      "text": "Patient was seated and relaxed"
    }
  ]
}

Interactions: read, search-type, create, update

Condition

Diagnoses, problems, and health concerns.

Example Condition

{
  "resourceType": "Condition",
  "id": "507f1f77bcf86cd799439013",
  "clinicalStatus": {
    "coding": [
      {
        "system": "http://terminology.hl7.org/CodeSystem/condition-clinical",
        "code": "active"
      }
    ]
  },
  "verificationStatus": {
    "coding": [
      {
        "system": "http://terminology.hl7.org/CodeSystem/condition-ver-status",
        "code": "confirmed"
      }
    ]
  },
  "code": {
    "coding": [
      {
        "system": "http://snomed.info/sct",
        "code": "44054006",
        "display": "Type 2 diabetes mellitus"
      }
    ]
  },
  "subject": {
    "reference": "Patient/507f1f77bcf86cd799439011"
  },
  "recordedDate": "2026-03-04T10:30:00Z",
  "note": [
    {
      "text": "Well-controlled with metformin"
    }
  ]
}

Clinical Statuses: active, recurrence, relapse, inactive, remission, resolved Interactions: read, search-type, create, update

AllergyIntolerance

Allergies and adverse reactions.

Example AllergyIntolerance

{
  "resourceType": "AllergyIntolerance",
  "id": "507f1f77bcf86cd799439014",
  "clinicalStatus": {
    "coding": [
      {
        "system": "http://terminology.hl7.org/CodeSystem/allergyintolerance-clinical",
        "code": "active"
      }
    ]
  },
  "verificationStatus": {
    "coding": [
      {
        "system": "http://terminology.hl7.org/CodeSystem/allergyintolerance-verification",
        "code": "confirmed"
      }
    ]
  },
  "type": "allergy",
  "category": ["food"],
  "criticality": "high",
  "code": {
    "coding": [
      {
        "system": "http://snomed.info/sct",
        "code": "227493005",
        "display": "Cashew nuts"
      }
    ]
  },
  "patient": {
    "reference": "Patient/507f1f77bcf86cd799439011"
  },
  "recordedDate": "2026-03-04T10:30:00Z",
  "reaction": [
    {
      "substance": {
        "text": "Cashew nuts"
      },
      "manifestation": [
        {
          "text": "Hives"
        }
      ],
      "severity": "moderate",
      "description": "Hives and skin rash"
    }
  ]
}

Categories: food, medication, environment, biologic Criticality: low, high, unable-to-assess Interactions: read, search-type, create, update

MedicationRequest

Prescription and medication orders.

Example MedicationRequest

{
  "resourceType": "MedicationRequest",
  "id": "507f1f77bcf86cd799439015",
  "status": "active",
  "intent": "order",
  "medicationCodeableConcept": {
    "coding": [
      {
        "system": "http://www.nlm.nih.gov/research/umls/rxnorm",
        "code": "860975",
        "display": "Metformin 500 MG Oral Tablet"
      }
    ]
  },
  "subject": {
    "reference": "Patient/507f1f77bcf86cd799439011"
  },
  "authoredOn": "2026-03-04T10:30:00Z",
  "dosageInstruction": [
    {
      "text": "Take 1 tablet by mouth twice daily"
    }
  ],
  "reasonCode": [
    {
      "text": "Type 2 diabetes"
    }
  ]
}

Status Values: active, on-hold, cancelled, completed, stopped Interactions: read, search-type, create, update

Encounter

Clinical visits and episodes of care.

Example Encounter

{
  "resourceType": "Encounter",
  "id": "507f1f77bcf86cd799439016",
  "status": "finished",
  "class": {
    "code": "AMB"
  },
  "type": [
    {
      "coding": [
        {
          "system": "http://snomed.info/sct",
          "code": "185349003",
          "display": "Outpatient visit"
        }
      ]
    }
  ],
  "subject": {
    "reference": "Patient/507f1f77bcf86cd799439011"
  },
  "period": {
    "start": "2026-03-04T10:00:00Z",
    "end": "2026-03-04T10:30:00Z"
  },
  "reasonCode": [
    {
      "text": "Routine follow-up"
    }
  ],
  "location": [
    {
      "location": {
        "display": "Primary care clinic"
      }
    }
  ],
  "serviceProvider": {
    "display": "General Medicine"
  }
}

Status Values: planned, arrived, in-progress, finished Interactions: read, search-type, create, update

Appointment

Scheduled appointments with slot-based booking.

Example Appointment

{
  "resourceType": "Appointment",
  "id": "507f1f77bcf86cd799439017",
  "status": "booked",
  "serviceCategory": [
    {
      "text": "Follow-up"
    }
  ],
  "description": "Diabetes follow-up visit",
  "start": "2026-03-15T09:00:00Z",
  "end": "2026-03-15T09:15:00Z",
  "minutesDuration": 15,
  "participant": [
    {
      "actor": {
        "reference": "Patient/507f1f77bcf86cd799439011"
      },
      "status": "accepted"
    },
    {
      "actor": {
        "reference": "Practitioner/507f1f77bcf86cd799439020",
        "display": "Dr. Jane Doe"
      },
      "status": "accepted"
    }
  ],
  "reasonCode": [
    {
      "text": "Diabetes management"
    }
  ],
  "comment": "Patient prefers morning appointments"
}

Status Values: booked, arrived, checked-in, fulfilled, cancelled, noshow, waitlist Scheduling Rules:

15-minute slots only
Monday-Saturday, 09:00-12:00
Conflict detection enforced

Interactions: read, search-type, create, update

Task

Care coordination tasks and workflows.

Example Task

{
  "resourceType": "Task",
  "id": "507f1f77bcf86cd799439018",
  "status": "requested",
  "intent": "order",
  "priority": "routine",
  "code": {
    "text": "Care coordination"
  },
  "description": "Schedule HbA1c follow-up lab work",
  "for": {
    "reference": "Patient/507f1f77bcf86cd799439011"
  },
  "owner": {
    "reference": "Practitioner/507f1f77bcf86cd799439020",
    "display": "Dr. Jane Doe"
  },
  "authoredOn": "2026-03-04T10:30:00Z",
  "executionPeriod": {
    "end": "2026-03-11T23:59:59Z"
  },
  "note": [
    {
      "text": "Patient has recent prescription changes"
    }
  ]
}

Status Values: requested, accepted, in-progress, on-hold, completed, cancelled Priority Levels: routine, urgent, asap, stat Task Categories:

Care coordination
Medication reconciliation
Lab follow-up
Preventive screening
Discharge outreach
Referral management

Interactions: read, search-type, create, update

Search Parameters

OmniEHR supports the following search parameters:

Patient Search

GET /api/fhir/Patient?identifier=1000042

Resource-Specific Search

By Patient
By Date Range
By Practitioner
By Status

GET /api/fhir/Observation?subject=Patient/507f1f77bcf86cd799439011
GET /api/fhir/Condition?subject=Patient/507f1f77bcf86cd799439011
GET /api/fhir/MedicationRequest?subject=Patient/507f1f77bcf86cd799439011

GET /api/fhir/Appointment?from=2026-03-01T00:00:00Z&to=2026-03-31T23:59:59Z

GET /api/fhir/Appointment?practitioner=Practitioner/507f1f77bcf86cd799439020
GET /api/fhir/Task?owner=Practitioner/507f1f77bcf86cd799439020

GET /api/fhir/Task?status=requested
GET /api/fhir/Task?for=Patient/507f1f77bcf86cd799439011&status=in-progress

Bundle Responses

All search operations return FHIR Bundle resources:

Searchset Bundle

{
  "resourceType": "Bundle",
  "type": "searchset",
  "id": "550e8400-e29b-41d4-a716-446655440000",
  "total": 2,
  "timestamp": "2026-03-04T10:30:00Z",
  "entry": [
    {
      "fullUrl": "https://your-server/api/fhir/Patient/507f1f77bcf86cd799439011",
      "resource": {
        "resourceType": "Patient",
        "id": "507f1f77bcf86cd799439011",
        // ... resource content
      },
      "search": {
        "mode": "match"
      }
    },
    {
      "fullUrl": "https://your-server/api/fhir/Patient/507f1f77bcf86cd799439012",
      "resource": {
        "resourceType": "Patient",
        "id": "507f1f77bcf86cd799439012",
        // ... resource content
      },
      "search": {
        "mode": "match"
      }
    }
  ]
}

Database Models

All FHIR resources are stored in MongoDB with indexed fields for efficient querying:

Patient Model Indexes

patientSchema.index({ "identifier.value": 1 });
patientSchema.index({ pid: 1 }, { unique: true, sparse: true });
patientSchema.index({ createdAt: -1 });

Appointment Model Indexes

appointmentSchema.index({ "patient.reference": 1, start: -1 });
appointmentSchema.index({ practitionerUserId: 1, start: 1, end: 1 });
appointmentSchema.index({ start: 1 });

Task Model Indexes

taskSchema.index({ "for.reference": 1, dueDate: 1 });
taskSchema.index({ ownerUserId: 1, status: 1, dueDate: 1 });

FHIR Mapper Service

OmniEHR includes a comprehensive FHIR mapper service to convert between FHIR resources and database documents:

fhirMapper.js

// Convert FHIR resource to database document
export const patientResourceToDoc = (resource) => {
  if (resource.resourceType !== "Patient") {
    throw new ApiError(400, "Expected a Patient resource");
  }
  
  const name = resource.name?.[0] || {};
  const givenName = name.given?.[0] || "";
  const familyName = name.family || "";
  const phone = pickTelecom(resource.telecom, "phone");
  const email = pickTelecom(resource.telecom, "email");
  const address = resource.address?.[0] || {};
  
  return {
    resourceType: "Patient",
    identifier: resource.identifier || [],
    active: resource.active !== false,
    gender: resource.gender || "unknown",
    birthDate: dateOnlyToDate(resource.birthDate),
    phi: {
      givenName: encryptPhi(givenName),
      familyName: encryptPhi(familyName),
      phone: encryptPhi(phone),
      email: encryptPhi(email),
      line1: encryptPhi(address.line?.[0] || ""),
      city: encryptPhi(address.city || ""),
      state: encryptPhi(address.state || ""),
      postalCode: encryptPhi(address.postalCode || "")
    }
  };
};

// Convert database document to FHIR resource
export const patientDocToResource = (doc) => {
  const phi = doc.phi || {};
  const givenName = decryptPhi(phi.givenName);
  const familyName = decryptPhi(phi.familyName);
  const phone = decryptPhi(phi.phone);
  const email = decryptPhi(phi.email);
  
  return {
    resourceType: "Patient",
    id: doc._id.toString(),
    identifier: doc.identifier || [],
    active: doc.active !== false,
    name: [{
      family: familyName,
      given: givenName ? [givenName] : []
    }],
    telecom: [
      ...(phone ? [{ system: "phone", value: phone }] : []),
      ...(email ? [{ system: "email", value: email }] : [])
    ],
    gender: doc.gender || "unknown",
    birthDate: toDateOnly(doc.birthDate),
    address: // ... address mapping
  };
};

Validation

All resources are validated using Zod schemas before persistence:

validation.js

import { z } from "zod";

export const patientResourceSchema = z.object({
  resourceType: z.literal("Patient"),
  identifier: z.array(z.object({
    system: z.string().optional(),
    value: z.string()
  })).optional(),
  active: z.boolean().optional(),
  name: z.array(z.object({
    family: z.string(),
    given: z.array(z.string()).optional()
  })),
  telecom: z.array(z.object({
    system: z.string(),
    value: z.string()
  })).optional(),
  gender: z.enum(["male", "female", "other", "unknown"]).optional(),
  birthDate: z.string().optional(),
  address: z.array(z.object({
    line: z.array(z.string()).optional(),
    city: z.string().optional(),
    state: z.string().optional(),
    postalCode: z.string().optional()
  })).optional()
});

Next Steps

Patient Management

Learn about patient registry and demographics

Scheduling

Explore appointment scheduling system

Clinical Workflows

View task management and care coordination

API Reference

Complete API documentation

Get Started

Core Features

Security & Compliance

Deployment

Supported Resources

Patient

Observation

Condition

AllergyIntolerance

MedicationRequest

Encounter

Appointment

Task

FHIR Capability Statement

Resource Details

Patient

Observation

Condition

AllergyIntolerance

MedicationRequest

Encounter

Appointment

Task

Search Parameters

Patient Search

Resource-Specific Search

Bundle Responses

Database Models

FHIR Mapper Service

Validation

Next Steps

Patient Management

Scheduling

Clinical Workflows

API Reference

Build docs developers (and LLMs) love

Get Started

Core Features

Security & Compliance

Deployment

Documentation Index

​Supported Resources

Patient

Observation

Condition

AllergyIntolerance

MedicationRequest

Encounter

Appointment

Task

​FHIR Capability Statement

​Resource Details

​Patient

​Observation

​Condition

​AllergyIntolerance

​MedicationRequest

​Encounter

​Appointment

​Task

​Search Parameters

​Patient Search

​Resource-Specific Search

​Bundle Responses

​Database Models

​FHIR Mapper Service

​Validation

​Next Steps

Patient Management

Scheduling

Clinical Workflows

API Reference

Build docs developers (and LLMs) love

Supported Resources

FHIR Capability Statement

Resource Details

Patient

Observation

Condition

AllergyIntolerance

MedicationRequest

Encounter

Appointment

Task

Search Parameters

Patient Search

Resource-Specific Search

Bundle Responses

Database Models

FHIR Mapper Service

Validation

Next Steps