Research Memory Protocol Template

Chinese documentation: README.zh-CN.md.

Local-first research memory protocol for AI agents, Obsidian, and MCP.

This template helps researchers manage cross-session project memory without treating AI chat history as the source of truth.

What This Solves

• Agents forget project context across sessions.

• Old project files are repeatedly reprocessed or converted.

• Multiple versions of figures, manuscripts, and reports become hard to track.

• AI-generated content can be mistaken for verified research evidence.

• Different agents need a shared protocol, not tool-specific memory.

Related MCP server: obsidian-mcp

Core Idea

Obsidian Vault = source of truth
Project Hub / Registry = structured project memory
MCP server = controlled read/write tools
Agent memory = optional recall layer, not evidence

Repository Layout

research-memory-protocol-template/
  mcp/
    research-memory-mcp.mjs
  templates/
    BOOTSTRAP.md
    global-research-memory-protocol.md
    external-project-path-map.md
    project-memory-template.md
    figure-registry-template.md
    task-summary-template.md
    .research-memory.md.template
  examples/
    fake-obsidian-vault/
    fake-external-project/
  config/
    opencode.example.json
    pi-mcp-servers.example.json
  docs/
    setup.md
    workflow.md
    safety.md

Quick Start

Choose one setup mode:

• MCP mode: for agents that support MCP, such as opencode or Pi agent.

• No-MCP file protocol mode: for any agent that can read and edit local files.

Both modes use the same Obsidian Markdown files as source of truth.

See:

• MCP setup

• No-MCP setup

• Agent prompts

MCP Quick Start

1. Copy templates/BOOTSTRAP.md to:

mkdir -p ~/.research-memory
cp templates/BOOTSTRAP.md ~/.research-memory/BOOTSTRAP.md

2. Copy protocol files into your Obsidian research system:

mkdir -p "<your-vault>/research-memory-vault/00-control"
cp templates/global-research-memory-protocol.md "<your-vault>/research-memory-vault/00-control/"
cp templates/external-project-path-map.md "<your-vault>/research-memory-vault/00-control/"

3. Configure environment variables:

export RESEARCH_MEMORY_ROOT="<your-vault>/research-memory-vault"
export RESEARCH_MEMORY_BOOTSTRAP="$HOME/.research-memory/BOOTSTRAP.md"

4. Add the MCP server to your agent:

node /path/to/research-memory-protocol-template/mcp/research-memory-mcp.mjs

Agent Prompt

Use this short prompt at the start of a session:

Use the research_memory MCP. First call read_bootstrap, then detect_project, then read_project_memory for the current project. Follow the research memory protocol: do not fabricate, do not move old files, do not delete figures automatically, prefer summaries and registries before deep-reading source files, and write back working memory with append_task_summary at the end. Final conclusions require my confirmation.

MCP Tools

• read_bootstrap

• detect_project

• read_project_memory

• append_task_summary

• append_figure_version

• list_projects

• file_fingerprint

Install from npm

After npm publication:

npm install -g research-memory-protocol-template
research-memory-mcp

Or use it through npx:

npx research-memory-protocol-template

Safety Model

The MCP server can write working memory, not verified conclusions.

Allowed automatic writeback:

• Task summaries

• Materials read

• Files created or modified

• Pending verification items

• Evidence gaps

• Figure version rows

Requires user confirmation:

• Final research conclusions

• Statistical interpretations

• Medical conclusions

• Literature evidence grades

• Manuscript-ready claims

Privacy

Do not publish your real Obsidian Vault, unpublished data, manuscripts, API keys, patient data, or real project paths.

This repository contains only templates and fake examples.