Fhir Mcp Server

general MCP Server

FHIR MCP Server – helping you expose any FHIR Server or API as a MCP Server.

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Who Is This For?

Healthcare software engineers and API developers building applications that integrate with FHIR-compliant systems. Clinical data managers and interoperability specialists who need programmatic access to standardized medical records. Backend developers working on health platforms benefit from having a structured interface to query, validate, and transform FHIR resources without manual protocol implementation.

Use Cases

Query and retrieve standardized patient records

Access patient data stored in FHIR format through Claude, enabling natural language queries against medical records. Useful for building clinical decision support tools or extracting relevant patient information for analysis.

Validate FHIR resource compliance

Ensure medical data payloads conform to FHIR specifications before persisting to production systems. Helps catch schema violations and malformed resources early in the development pipeline.

Transform legacy data to FHIR

Convert non-standard medical data formats into compliant FHIR resources. Facilitates data migration projects and system integration between healthcare platforms with different data models.

Integrate health data into AI workflows

Leverage Claude's reasoning capabilities with structured medical data to generate clinical summaries, identify patterns, or support documentation automation within HIPAA-aware applications.

Frequently Asked Questions

Does this MCP server handle authentication and HIPAA compliance?

The MCP server provides FHIR data handling capabilities, but authentication and HIPAA compliance depend on your deployment context and how you configure access controls. You must implement security measures appropriate for handling protected health information in your own infrastructure.

What FHIR versions are supported?

Specific version support isn't detailed in the current documentation. Check the server's configuration options or repository to confirm which FHIR versions (R4, STU3, etc.) your deployment supports.

Can I use this to connect to existing EHR systems?

This MCP server handles FHIR data format translation and validation. Connecting to EHR systems requires those systems to expose FHIR APIs or implement FHIR export capabilities on their end; this server bridges Claude to FHIR-formatted data.

How do I get started integrating this with my Claude application?

You'll run the MCP server locally or remotely, then configure Claude or your application to connect via the Model Context Protocol. Detailed setup instructions should be in the server's documentation or GitHub repository.

Available Tools (36)

LOINC_PASSWORD

LOINC account password

request_generic_resource

Any FHIR Resource

MASTER_KEY

Master encryption key

LOINC_ENDPOINT

LOINC API search endpoint

Variable

Description

PINECONE_API_KEY

Pinecone API key

EMBEDDING_MODEL

Hugging Face embedding model name

get_capabilities

Retrieves metadata about a specified FHIR resource type, including its supported search parameters and custom operations.

type

The FHIR resource type name (e.g., "ServiceRequest", "Appointment", "HealthcareService").

searchParam

A mapping of FHIR search parameter names to their desired values (e.g., {"category":"laboratory","issued:"2025-05-01"}).

read

Performs a FHIR "read" interaction to retrieve a single resource instance by its type and resource ID, optionally refining the response with search parameters or custom operations.

operation

The name of a custom FHIR operation or extended query defined for the resource (e.g., "$expand").

create

Executes a FHIR "create" interaction to persist a new resource of the specified type.

update

Performs a FHIR "update" interaction by replacing an existing resource instance's content with the provided payload.

delete

Execute a FHIR "delete" interaction on a specific resource instance.

id

The logical ID of a specific FHIR resource instance.

search

Executes a standard FHIR search interaction on a given resource type, returning a bundle or list of matching resources.

payload

The complete JSON representation of the FHIR resource, containing all required elements and any optional data.

request_observation_resource

Observation

request_document_reference_resource

Manage FHIR DocumentReference resources

No

<p align="right">(<a href="#readme-top">back to top</a>)</p> ## 🛠️ MCP Tools The FHIR MCP Server provides a comprehensive set of tools for interacting with FHIR resources and document management: ### FHIR Resource Tools

request_medication_resource

Medication

search_pinecone

Performs semantic search across indexed documents using vector embeddings

request_condition_resource

Condition

add_document_to_pinecone

Ingests documents into the vector database for semantic search

request_allergy_intolerance_resource

AllergyIntolerance

request_encounter_resource

Encounter

get_loinc_codes

Retrieves standardized LOINC codes for medical observations and laboratory tests

request_patient_resource

Patient

Tool

Description

loinc-user

No

request_immunization_resource

Immunization

request_family_member_history_resource

FamilyMemberHistory

code

accepts a raw LOINC code (`8867-4`) **or** a friendly name

response_filter_fhirpaths

(Optional) An array of FHIRPath expressions (e.g., `["Patient.name", "Observation.valueQuantity"]`) to filter the returned single resource (or entries when using custom operations like `$everything`).

get_user

Retrieves the currently authenticated user's FHIR resource (for example the linked `Patient` resource) and returns a concise profile containing available demographic fields such as `id`, `name`, and `birthDate`.