Research Knowledge Base SOP

This repository contains a reusable SOP for building an AI-assisted research knowledge base. It focuses on paper discovery, PDF parsing, paper summaries, concept and entity indexing, research gaps, comparisons, and synthesis notes.

The repository is organized as a set of operating procedures and page templates. It is intended to be adapted to your own research area, tools, and publishing targets.

What This Is

• A workflow for turning papers into structured research notes.
• A directory convention for separating raw inputs, parsed material, wiki pages, and SOP documents.
• A set of templates for paper summaries, concepts, entities, gaps, comparisons, synthesis pages, and daily paper reports.
• A set of guardrails for source verification, human confirmation, and avoiding fabricated links or identifiers.

What This Is Not

• It is not a finished public research wiki.
• It does not include private paper PDFs, raw OCR outputs, or personal reading logs.
• It does not require a specific note-taking app, automation platform, or external document service.

Repository Map

.
├── CLAUDE.md                 # Agent-facing global SOP
├── INDEX-*.md                # Optional Dataview-style overview pages
├── docs/
│   ├── Workspace.md          # Docs map and workspace structure
│   ├── UserFocus.md          # Public template for focus preferences
│   ├── operation/            # Task procedures
│   └── pattern/              # Page templates
├── wiki/                     # Knowledge-base pages
├── raw/                      # Parsed paper outputs
└── downloads/                # Source PDFs and metadata

Recommended Public/Private Split

Safe to publish:

• README.md
• CLAUDE.md, after reviewing tool-specific instructions
• docs/
• empty or example INDEX-*.md files

Usually keep private or publish only as examples:

• downloads/
• raw/
• wiki/log.md
• full daily reports
• private focus preferences
• unpublished paper notes or drafts

How To Use

1. Read docs/Workspace.md for the workspace structure and document map.
2. Use CLAUDE.md as the global execution contract for an AI assistant.
3. For a task, read the corresponding file in docs/operation/.
4. When writing a page, use the corresponding template in docs/pattern/.
5. Keep source identifiers real and verifiable. Do not invent DOI, arXiv, OpenReview, Semantic Scholar, or other source IDs.

Customization Points

• Replace docs/UserFocus.md with your own current research interests.
• Adjust discovery sources in docs/operation/DailyPaperWorklist.md.
• Add or remove frontmatter fields to match your note-taking system.
• Replace optional publishing targets with your own export workflow.

License

Choose a license before publishing if you want others to reuse this SOP.