deep-search

Consolidate scholarly literature into a structured findings.md with a companion literature-map using PaperCLI retrieval.

11|1|Updated Feb 23, 2026
One-click install
npx skills add https://github.com/jimezsa/opencolab --skill deep-search-jimezsa
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: deep-search
Source: https://github.com/jimezsa/opencolab/tree/main/projects/SKILLS/deep-search
Command: npx skills add https://github.com/jimezsa/opencolab --skill deep-search-jimezsa

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Consolidates scattered scholarly literature into an evidence-grounded, end-to-end synthesis.

Core Features & Use Cases

  • Iterative multi-wave retrieval using PaperCLI to locate, download, and read relevant PDFs.
  • Equation-level analysis and structured extraction to produce a findings.md and a literature-map.
  • Companion literature-map diagram generation to visualize method families and evidence connections.
  • Use Case: For a topic like "deep learning in biology," run a full literature sweep and generate a defensible, cite-backed report.

Quick Start

Run a multi-wave literature search with PaperCLI on your topic and generate a findings.md report with a validated literature-map.

Frequently Asked Questions about deep-search

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

FAQPage Schema
What is a systematic literature review and how does evidence-backed synthesis work?

A systematic literature review consolidates scattered scholarly papers into an evidence-grounded synthesis. Evidence-backed synthesis works by performing multi-wave retrieval, deep reading PDFs, and structured cross-paper analysis to produce a defensible report.

How do I extract mathematical equations and key concepts from research PDFs?

To extract mathematical equations and key concepts from research PDFs, use a deep search process that downloads full texts and applies equation-level analysis. This yields structured findings and a literature-map diagram visualizing method families and evidence connections.

Does this literature discovery process require PaperCLI for PDF retrieval?

Yes, this literature discovery process requires PaperCLI as its retrieval backbone. PaperCLI is used to locate, download, and read relevant PDFs during the iterative multi-wave search phase before extracting findings and generating the literature-map.

Can I generate a literature map to visualize method families and evidence connections?

Yes, you can generate a companion literature-map diagram to visualize method families and evidence connections. This diagram is produced alongside a findings.md report after completing the structured cross-paper analysis of downloaded PDFs.

What is the best way to consolidate scattered scholarly literature into a defensible report?

The best way to consolidate scattered scholarly literature into a defensible report is through iterative multi-wave retrieval using PaperCLI. This method downloads PDFs, extracts key concepts and equations, and produces a validated findings.md with a companion literature-map.

When should I not use automated deep search for complex scientific questions?

Automated deep search for complex scientific questions is not suitable for simple lookups or non-scholarly sources. This approach is designed specifically for complex scientific queries requiring multi-wave retrieval, deep PDF reading, mathematical extraction, and structured cross-paper analysis.