cava-mcp 0.1.2

CaVa MCP server — read-only agentive access to OMOP vocab, cohorts, and clinical vocabularies.

cava-mcp

cava-mcp is an atomic, read-only MCP (Model Context Protocol) tool library for navigating the OMOP vocabularies. It exposes OMOP vocabulary lookups, embedding similarity search, cohort concept references, and system status as typed MCP tools that any MCP client can call — including cava-datahub, Claude Code, and autonomous agents.

Read-only. No patient-level data. No write operations.

What it exposes

Group	Tools
Concept	concept_get, concept_by_code, concept_ancestors, concept_descendants, concept_relationships, concept_equivalency_path, concept_path, concept_map_to_standard, concept_neighbors
Resolver	concept_ground (with parent_ids, scoring fields, and grounding_explanation)
Search	concept_search_exact, concept_search_fulltext, concept_navigate_to_standard
Embedding	embedding_index_status, embedding_neighbours, embedding_search, embedding_encode
Cohort	cohort_find_concept_references
System	system_status, system_vocabulary_catalogue

Tools are registered conditionally — if an adapter is not configured, its tools are simply not registered. system_status and system_vocabulary_catalogue are always registered so clients can always query adapter availability.

Quick start

uv venv
uv sync --extra dev --extra embedding-tools
uv run cava-mcp --config config/cava-mcp.example.yaml --describe

Start the server:

uv run cava-mcp --config config/cava-mcp.example.yaml

Example config

omop_graph:
  db_url: "postgresql+psycopg://user:pass@localhost:5432/omop"
  vocab_schema: omop_vocab

omop_emb:
  enabled: true
  backend_type: pgvector
  db_url: "postgresql+psycopg://user:pass@localhost:5432/omop"
  default_model_name: qwen3-embedding:0.6b
  api_base: "http://localhost:11434/v1"
  api_key: "ollama"

Install matrix

Use case	Extras
Core server only	none
Concept tools	concept-tools
Cohort tools	cohort-tools
Embedding tools (sqlite-vec)	embedding-tools
Embedding tools (pgvector)	embedding-pgvector
Embedding tools (FAISS sidecar)	embedding-faiss
All tool families	all-tools
All + pgvector embeddings	all-tools-pgvector
All + FAISS embeddings	all-tools-faiss
Development	dev
Development + all tools	dev-all

Layout

src/cava_mcp/
  adapters/          — omop_graph, omop_emb, oa_cohorts adapter classes
  base/              — DataHubServer, errors, results, SQL helpers
  tools/             — MCP tool registrations by domain
  config.py          — Pydantic config models (AppConfig, OmopGraphConfig, etc.)
  server.py          — Server factory and CLI entry point
config/              — Example YAML configs
_design/             — Architecture notes and spec documents
tests/               — Unit and integration tests

Adapter backends

• omop-graph — concept lookup, hierarchy traversal, full-text search
• omop-emb — embedding index (sqlite-vec, pgvector, or FAISS sidecar)
• OpenAnalytics cohorts — cohort concept reference queries (Phase N)

Companion repos

• cava-datahub — ACP orchestration layer that drives this tool substrate
• omop-graph — OMOP virtual knowledge graph library
• omop-emb — OMOP embedding index library