Harmonization via MCP

Provides a basic overview of available harmonization capabilities and how to accomplish them using the Rhino MCP.

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

Rhino's Harmonization 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 centralised at any point.

If you do not have the required permissions, you will not be able to perform the following actions.

Managing schemas

Schemas 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."

Browsing custom vocabularies

Look up standard custom concepts that have been added before constructing mappings. Or, you can upload your own custom vocabulary. 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 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 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 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."