---
type: MCP Server
title: mesa-mcp
description: The flagship MESA server — iRODS Data Store tools, OBO/OLS ontology AVUs, DataCite, and DuckLake metadata history.
tags:
  - mesa-mcp
  - python
  - irods
  - ontology
  - datacite
  - ducklake
generated:
  by: "claude/fable-5"
  at: "2026-07-18T00:00:00Z"
sources:
  - id: repo
    resource: "https://github.com/idss-mesa/mesa-mcp"
    title: "mesa-mcp source repository"
    author: "team:idss-mesa"
status: stable
stale_after: "2027-03-10T00:00:00Z"
---

# mesa-mcp

**Repo:** [idss-mesa/mesa-mcp](https://github.com/idss-mesa/mesa-mcp) · **Language:** Python 3.11+ · **Registered as:** `mesa-mcp`

The flagship MESA server. It bridges the CyVerse Data Store (iRODS) with ontology-driven
metadata management and exposes everything as MCP tools.

## Tool groups

| Prefix | What it does |
|---|---|
| `ds_*` | iRODS Data Store: list/read/write/move files, directories, AVUs, ACLs, tickets, rules, policies (drop-in compatible with [irods-mcp-server](https://idss-mesa.github.io/docs/servers/irods-mcp-server/)) |
| `mesa_ols_*` | Browse OBO/OLS ontologies: search terms, fetch hierarchies, generate AVU templates |
| `mesa_avu_*` | Apply ontology terms and DataCite fields as AVUs (with the CURIE in the `unit` slot) |
| `mesa_datacite_*` | DataCite metadata: template, validate, export, apply |
| `mesa_ducklake_*` | Metadata history: init a project, snapshot, list history, time-travel, diff (backed by [mesa-ducklake](https://idss-mesa.github.io/docs/servers/mesa-ducklake/)) |

## How MESA runs it

The installer creates a uv venv and installs `mesa-mcp` editable (alongside
`mesa-ducklake`), then registers the stdio entry point:

```bash
~/.mesa/.venv/bin/mesa-mcp --transport stdio
```

It is registered under the name `mesa-mcp` with every detected client — see
[Claude Code](https://idss-mesa.github.io/docs/claude-code/), [Codex CLI](https://idss-mesa.github.io/docs/codex/),
[Antigravity](https://idss-mesa.github.io/docs/antigravity/), or [OpenCode](https://idss-mesa.github.io/docs/opencode/) for the exact
registration each one gets.

## The AVU contract

Metadata is written as `(attribute, value, unit)` triples, where `unit` is reserved for the
ontology CURIE when the AVU came from OBO/OLS. Provenance (actor, source, ticket, rule) is
recorded in DuckLake columns, never folded into the triple.

## Configuration

Configuration precedence is **CLI flag > environment variable > YAML file > defaults**. The
defaults target anonymous public CyVerse access. See [Credentials](https://idss-mesa.github.io/docs/credentials/) and
[`.env.example`](https://github.com/idss-mesa/mesa-mcp/blob/main/.env.example) for the full set.

Full documentation lives in the repo under
[`docs/`](https://github.com/idss-mesa/mesa-mcp/tree/main/docs) (user / dev / deploy guides).