deep-research

Coordinate Zotero data with external databases to produce convergent literature syntheses.

Updated Mar 22, 2026
One-click install
npx skills add https://github.com/shusuke-ioku/r2 --skill deep-research-shusuke-ioku
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: deep-research
Source: https://github.com/shusuke-ioku/r2/tree/main/src/r2/template/.claude/skills/deep-research
Command: npx skills add https://github.com/shusuke-ioku/r2 --skill deep-research-shusuke-ioku

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

This skill orchestrates end-to-end literature surveys by integrating local Zotero RAG with external databases to deliver a structured synthesis.

Core Features & Use Cases

  • Discovery & indexing of local and external sources to build a comprehensive corpus.
  • Iterative discovery loop with search, snowball, triage, acquisition, and reading to convergence.
  • Thematic synthesis & reporting that maps literatures into themes and identifies gaps, with a ready-to-export report template.

Quick Start

Ask me to survey a topic, and I will run iterative discovery to produce a structured literature report.

Frequently Asked Questions about deep-research

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I automate a systematic literature survey using Zotero and external databases?

To automate a systematic literature survey, this skill coordinates local Zotero RAG with external databases like Semantic Scholar and OpenAlex. It runs an iterative discovery loop covering search, snowballing, triage, acquisition, and reading to generate a convergent thematic synthesis.

What is snowballing in literature review and how does it work with RAG?

Snowballing in literature review is the iterative discovery of new sources via citation tracking. This skill integrates local Zotero RAG with external datastores to automate snowballing, continuously searching and triaging references until the corpus reaches thematic convergence.

Do I need a specific Zotero setup to perform an end-to-end literature survey?

Yes, performing an end-to-end literature survey requires access to an indexed literature store using Zotero RAG. You also need access to external datastores like Semantic Scholar, OpenAlex, or Scopus, plus a structured report template for the final synthesis.

Can I use OpenAlex and Semantic Scholar for breadth surveys across multiple fields and time spans?

Yes, you can use OpenAlex and Semantic Scholar for breadth surveys across topics, fields, and time spans. This skill coordinates these external datastores with your local Zotero corpus to handle discovery, acquisition, reading, and thematic mapping.

What is the best way to map literature into themes and identify research gaps?

The best way to map literature into themes and identify research gaps is through thematic synthesis and reporting. This skill processes the acquired corpus to map literatures into themes, identify gaps, and generate a ready-to-export structured report.

What are the limitations of using automated RAG for literature discovery and triage?

Automated RAG for literature discovery depends heavily on the quality of your indexed Zotero store and external database coverage. Synthesis is limited by the indexed corpus and requires a structured report template to format the final thematic gaps and reading outputs.