> For the complete documentation index, see [llms.txt](https://docs.rhinofcp.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.rhinofcp.com/using-the-rhino-mcp-server/schemas-and-harmonization-via-mcp.md).

# Schemas & Harmonization via MCP

This article describes what you can do in the Harmonization capability area, with example prompts for each action.

Rhino's [Harmonization](/data-harmonization/overview.md) tools allow you to map source datasets from participating sites to a target schema or standard medical vocabulary (e.g., OMOP, FHIR), and perform transformations in a federated manner. The raw and transformed data stay at each site — no data is centralized at any point.

{% hint style="warning" %}
If you do not have the required permissions, you will not be able to perform the following actions.
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## Managing schemas

[Schemas](/data-schemas/what-is-a-data-schema.md) define the structure that source and target data are mapped to. You can list, inspect, create, and delete schemas through conversation.

* *"What data schemas are available in my workgroup?"*
* *"Show me the columns defined in the OMOP patient target."*
* *"Create a new target schema called 'Standard Admissions' with columns for patient\_id, admission\_date, diagnosis\_code, and los\_days."*
* *"Delete the 'Draft Schema v1' schema."*

{% hint style="info" %}
**AI tools are only as good as the information they are given**, for this reason Rhino enables augmenting data schemas by including a description for each field. 

Auto-generated schemas have empty descriptions and default most columns Float, or String. 

While LLMs like Claude can draft column descriptions and proposed definitions, human ownership and curation are essential—automatically bootstrapping a semantic layer from raw tables or query logs risks encoding existing ambiguities into source-of-truth definitions. 

A curated semantic layer (descriptions, correct types, valid values, concept IDs and join keys on every schema) is what lets a clinical question map to the right column the first time.
{% endhint %}

## Browsing custom vocabularies

Look up standard custom concepts that have been added before constructing mappings. Or, you can upload your own [custom vocabulary](/data-harmonization/semantic-mapping/custom-vocabularies.md). Some example vocabularies that you might want to add include OMOP CDM, SNOMED CT, ICD-10, LOINC, and RxNorm.

* *"Find the SNOMED concept ID for 'type 2 diabetes mellitus'."*
* *"Look up ICD-10 codes related to heart failure."*
* *"What is the LOINC code for serum creatinine?"*
* *"Search the RxNorm vocabulary for metformin."*

## Creating semantic mappings

Use AI-assisted [semantic mapping](/data-harmonization/semantic-mapping.md) to generate suggested mappings from your source dataset column values to standard vocabulary concepts. Suggestions come with confidence scores for you to review before applying.

* *"Which columns in my dataset need vocabulary-based term mapping to fit the target schema?"*
* *"Create a semantic mapping for the diagnosis\_code column using the ICD vocabulary."*
* *"Is my semantic mapping for the diagnosis codes ready to use?"*

## Creating syntactic mappings

[Syntactic mapping](/data-harmonization/syntactic-mapping.md) defines the structural field-level mapping between your source dataset's columns and the target schema's columns, independent of medical concept meaning.

* *"Create a syntactic mapping from my admissions dataset to the Standard Admissions schema."*
* *"Auto-generate the field transformations for the Standard Admissions syntactic mapping."*
* *"Show me the current configuration of the Standard Admissions syntactic mapping."*
* *"The date format transformation is wrong - change it to use ISO 8601 format in the Standard Admissions mapping."*
* *"Update the description of the Standard Admissions mapping to 'Admissions to OMOP v2'."*

## Running the harmonization pipeline

Once your semantic and syntactic mappings are in place, [run the full harmonization pipeline](/data-harmonization/executing-the-transformation.md) to transform the source dataset to the target schema across all sites.

* *"Run the harmonization on the admissions dataset using the Standard Admissions mapping."*
* *"Transform the admissions data and check the status of the harmonization run."*


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