academic-research-wiki

Ingest academic sources into a Markdown wiki with evidence tracing.

Updated Apr 9, 2026
One-click install
npx skills add https://github.com/emilmirzayev/academic-llm-wiki --skill academic-research-wiki
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: academic-research-wiki
Source: https://github.com/emilmirzayev/academic-llm-wiki/tree/main
Command: npx skills add https://github.com/emilmirzayev/academic-llm-wiki --skill academic-research-wiki

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This Skill helps researchers build and maintain a persistent, source-grounded markdown knowledge base for literature review and paper analysis, ensuring traceability back to raw materials. It enables ingesting Obsidian Web Clipper markdown exports and paper PDFs, converting PDFs to Markdown with MarkItDown, and extracting theories, constructs, relationships, mechanisms, methods, findings, and contributions.

Core Features & Use Cases

  • Ingest Obsidian Web Clipper markdown exports and paper PDFs, convert PDFs to Markdown with MarkItDown to create readable, linked pages.
  • Extract and organize core research elements: theories, constructs, mechanisms, methods, findings, and contributions, with transparent provenance to sources.
  • Maintain a centralized index and a _meta/source-registry.md to track sources, versions, and ingestion status.
  • Enable search, cross-linking, and reuse for theory/construct/mechanism pages across papers.

Quick Start

Ingest a provided Obsidian Web Clipper markdown export and its associated PDF to create a new paper page with source links and evidence-ready sections.

Frequently Asked Questions about academic-research-wiki

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

FAQPage Schema
How do I build a source-grounded literature review wiki in Obsidian?

To build a source-grounded literature review wiki, ingest Obsidian Web Clipper markdown exports and paper PDFs to create linked pages. The wiki uses YAML frontmatter for metadata and a centralized source registry to track all ingested academic sources.

How do I convert academic paper PDFs to Markdown for knowledge management?

You can convert academic paper PDFs to Markdown for knowledge management by processing them through MarkItDown during ingestion. This creates readable, linked markdown pages that extract theories, constructs, methods, and findings while separating explicit claims from inferences.

What is evidence traceability in an academic knowledge base?

Evidence traceability in an academic knowledge base is the continuous linking of extracted research elements back to raw source materials. It ensures that theories, mechanisms, and findings tracked in markdown pages maintain provenance to their original paper PDFs or web exports.

Can I use Obsidian Web Clipper exports for academic literature reviews?

Yes, you can use Obsidian Web Clipper exports for academic literature reviews by ingesting them directly into the knowledge base. The system applies canonical naming to raw sources and tracks ingestion status in a central registry to organize web-captured content.

Does this knowledge management workflow separate explicit source claims from inferences?

Yes, this knowledge management workflow explicitly separates source claims from agent inferences. Extracted research elements like constructs and mechanisms are organized with transparent provenance, ensuring distinct boundaries between original paper claims and analytical additions.

When should I use a markdown wiki for mechanism tracing and theory building?

You should use a markdown wiki for mechanism tracing and theory building when you need to cross-link theories, constructs, and methods across multiple papers. It provides a persistent, searchable structure that tracks source versions and maintains evidence-ready sections.