# Mira Annotation

Annotate Markdown documents with MIRA research objects and source-local relations.

- Repository: https://github.com/stencila/stencila (914 stars)
- Category: Writing
- License: Apache-2.0
- Last updated: 2026-11-01
- Runs scripts: no, instructions only

## Install

Claude Code: `npx skills add stencila/stencila --skill mira-annotation -g -a claude-code -y`
Codex: `npx skills add stencila/stencila --skill mira-annotation -g -a codex -y`
Cursor: `npx skills add stencila/stencila --skill mira-annotation -g -a cursor -y`
Gemini CLI: `npx skills add stencila/stencila --skill mira-annotation -g -a gemini-cli -y`
Claude Code plugin marketplace: `/plugin marketplace add stencila/stencila`

## Description

Annotate Markdown documents with MIRA research objects and source-local relations. Use for md, smd, qmd, and myst files when identifying claims, evidence, questions, protocols, requests, typed claims, and relation attributes while preserving the original Markdown flavor and author wording. Not for general copyediting, prose rewriting, or extracting a separate knowledge graph without annotating the source.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

## Overview

Annotate Markdown documents with MIRA research objects and relations. Identify claims, evidence, questions, protocols, requests, and related scholarly objects in the source text, then wrap or mark those passages using syntax that is idiomatic for the document's Markdown flavor.

This skill is for semantic research-object annotation, not copyediting. Preserve the author's wording and document structure unless the user explicitly asks for rewriting.

## Required Inputs

| Input | Required | Description |
|---|---|---|
| Target Markdown content or file path | Required | The Markdown text or document to annotate |
| Markdown flavor or file extension | Optional | One of `.md`, `.smd`, `.qmd`, or `.myst`; infer from the file path and local syntax when absent |
| Annotation scope | Optional | Whether to annotate the entire document, a section, or only selected passages |
| Object vocabulary preferences | Optional | Any user or project preference for specific object types, typed claims, ids, or relation style |
| Delivery mode | Optional | Whether to edit the source file, return annotated Markdown, or provide an annotation plan first |

When used standalone, these inputs come from the user or the agent's prompt. When used within a workflow, the workflow's stage prompt will specify how to obtain them.

## Outputs

The rest: https://github.com/stencila/stencila/blob/HEAD/.stencila/skills/mira-annotation/SKILL.md